X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.2
Temperature 298.0
Details 0.9 M sodium citrate, 0.1 M imidazole, 25 mM 2-mercaptoethanol, and 2 mM CoA, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.65 α = 90
b = 110.6 β = 90
c = 119.92 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2010-07-02
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B

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
1.94 50 97.3 0.214 0.214 -- 9.4 64164 64164 -- -3.0 --
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)
1.94 2.01 94.8 0.6 0.6 3.9 6.5 6136

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 1.95 42.815 -- 0.0 -- 60824 3021 91.7 -- 0.1609 0.1585 0.2059 RANDOM
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 1.9498 2.0195 5207 254 4953 0.1776 0.2601 -- 79.0
X Ray Diffraction 2.0195 2.1004 5753 285 5468 0.1743 0.2502 -- 88.0
X Ray Diffraction 2.1004 2.196 5836 291 5545 0.168 0.2253 -- 89.0
X Ray Diffraction 2.196 2.3117 5906 308 5598 0.1666 0.2276 -- 90.0
X Ray Diffraction 2.3117 2.4566 6028 286 5742 0.1617 0.2169 -- 92.0
X Ray Diffraction 2.4566 2.6462 6098 308 5790 0.1618 0.2158 -- 92.0
X Ray Diffraction 2.6462 2.9125 6180 303 5877 0.1682 0.2096 -- 93.0
X Ray Diffraction 2.9125 3.3338 6375 323 6052 0.1665 0.2111 -- 96.0
X Ray Diffraction 3.3338 4.1996 6618 326 6292 0.1431 0.172 -- 99.0
X Ray Diffraction 4.1996 42.8255 6823 337 6486 0.147 0.1872 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.5496
Anisotropic B[1][1] -2.0166
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.9185
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.9019
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.099
f_plane_restr 0.005
f_chiral_restr 0.072
f_angle_d 1.034
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7686
Nucleic Acid Atoms 0
Heterogen Atoms 113
Solvent Atoms 745

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.6.3_473) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction