X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details 1 M sodium citrate, 0.1 M imidazole, 25 mM 2-mercaptoethanol, and 2 mM CoA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.42 α = 90
b = 110.85 β = 90
c = 120.37 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 -- 2009-12-06
Diffraction Radiation
Monochromator Protocol
C(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 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
1.7 50 99.8 0.105 0.105 -- 13.3 99312 99312 -- -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)
1.7 1.73 97.6 0.542 0.542 2.9 8.4 4801

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 1.7 28.8 -- 0.0 -- 95944 4802 96.26 -- 0.1577 0.1557 0.1939 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 1.7004 1.7612 8489 443 8046 0.2231 0.2674 -- 86.0
X Ray Diffraction 1.7612 1.8317 9083 438 8645 0.1921 0.2596 -- 92.0
X Ray Diffraction 1.8317 1.915 9339 472 8867 0.1638 0.2172 -- 95.0
X Ray Diffraction 1.915 2.0159 9466 474 8992 0.1584 0.2224 -- 96.0
X Ray Diffraction 2.0159 2.1422 9650 477 9173 0.1501 0.1953 -- 97.0
X Ray Diffraction 2.1422 2.3075 9745 506 9239 0.1527 0.2002 -- 98.0
X Ray Diffraction 2.3075 2.5396 9813 481 9332 0.1492 0.1812 -- 99.0
X Ray Diffraction 2.5396 2.9068 9939 490 9449 0.1599 0.2067 -- 99.0
X Ray Diffraction 2.9068 3.6611 10041 506 9535 0.1488 0.1682 -- 100.0
X Ray Diffraction 3.6611 28.8038 10379 515 9864 0.1453 0.1738 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.7524
Anisotropic B[1][1] -0.0306
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.7377
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.7071
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.924
f_plane_restr 0.005
f_chiral_restr 0.071
f_angle_d 1.044
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7768
Nucleic Acid Atoms 0
Heterogen Atoms 126
Solvent Atoms 1236

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