X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 289.0
Details ACETYL COA SYNTHETASE FROM CRYPTOCOCCUS NEOFORMANS (CRNEC.00629.A.FS11.PD00402) AT 10MG/ ML (IN 10 MM TRIS, PH = 7.5, 20 MM NACL) WAS SET UP IN SPARSE CRYSTALLIZATION TRIALS AT 16C. 0.5MM AC-AMS WAS ADDED TO THE PROTEIN SOLUTION AND INCUBATED FOR 5 MINUTES BEFORE SETTING UP TRIALS. CRYSTALS WERE PRODUCED BY SITTING DROP VAPOR DIFFUSION WITH AN EQUAL VOLUME COMBINATION OF THE PROTEIN/LIGAND IN AN OPTIMIZATION SCREEN BASED ON WIZARD 1 AND 2 SCREEN CONDITION E8 (13.18% W/V PEG8,000, 0.2M NACL, 0.1M NA/K PHOSPHATE PH6) AND CRYO-PROTECTED IN 20% ETHYLENE GLYCOL. CRYSTAL ID 284335C8, ZNI9-6, APS21-ID-G), PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 71.28 α = 110.33
b = 83.78 β = 105.81
c = 101.6 γ = 87.75
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2016-11-13
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-G 0.978560 APS 21-ID-G

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.5 50 98.5 0.073 -- -- 3.9 -- 72292 -- -3.0 51.82
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.5 2.56 97.8 0.588 -- 2.64 4.0 21134

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.5 32.099 -- 1.98 -- 72227 1999 98.64 -- 0.1548 0.1532 0.2087 --
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.4999 2.5624 -- 142 4975 0.2324 0.3322 -- 98.0
X Ray Diffraction 2.5624 2.6316 -- 142 5000 0.218 0.2719 -- 98.0
X Ray Diffraction 2.6316 2.709 -- 142 4994 0.2054 0.2902 -- 98.0
X Ray Diffraction 2.709 2.7964 -- 143 4995 0.1977 0.2618 -- 98.0
X Ray Diffraction 2.7964 2.8963 -- 142 5034 0.1874 0.2401 -- 98.0
X Ray Diffraction 2.8963 3.0122 -- 141 4968 0.1963 0.3128 -- 99.0
X Ray Diffraction 3.0122 3.1492 -- 144 5047 0.1736 0.2271 -- 99.0
X Ray Diffraction 3.1492 3.315 -- 143 4990 0.1712 0.2227 -- 99.0
X Ray Diffraction 3.315 3.5225 -- 143 5034 0.1613 0.2116 -- 99.0
X Ray Diffraction 3.5225 3.7941 -- 143 5031 0.1454 0.2057 -- 99.0
X Ray Diffraction 3.7941 4.1751 -- 143 5070 0.1301 0.1929 -- 99.0
X Ray Diffraction 4.1751 4.7776 -- 144 5027 0.1116 0.1738 -- 99.0
X Ray Diffraction 4.7776 6.0128 -- 144 5079 0.1283 0.1474 -- 99.0
X Ray Diffraction 6.0128 32.1013 -- 143 4984 0.14 0.1806 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 51.82
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.058
f_angle_d 0.903
f_plane_restr 0.007
f_dihedral_angle_d 15.18
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 15189
Nucleic Acid Atoms 0
Heterogen Atoms 121
Solvent Atoms 399

Software

Software
Software Name Purpose
XDS data reduction
XSCALE data scaling
PHENIX refinement version: (1.11.1_2575: 000)