X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

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 10 mM dethiaacetyl-CoA, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.49 α = 90
b = 104.05 β = 90
c = 120.13 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 -- 2011-12-03
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
2.64 50 100.0 0.14 0.14 -- 14.7 29835 29835 -- -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)
2.65 2.7 100.0 0.754 0.754 6.2 14.9 1441

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 2.644 43.531 -- 0.0 -- 29775 1489 99.93 -- 0.1709 0.1679 0.2256 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 2.6443 2.7296 2663 133 2530 0.2221 0.2966 -- 100.0
X Ray Diffraction 2.7296 2.8271 2642 132 2510 0.2134 0.275 -- 100.0
X Ray Diffraction 2.8271 2.9403 2681 134 2547 0.2013 0.3017 -- 100.0
X Ray Diffraction 2.9403 3.0741 2671 133 2538 0.1959 0.2596 -- 100.0
X Ray Diffraction 3.0741 3.2361 2664 134 2530 0.1878 0.2799 -- 100.0
X Ray Diffraction 3.2361 3.4388 2698 134 2564 0.1848 0.2589 -- 100.0
X Ray Diffraction 3.4388 3.7042 2681 135 2546 0.1769 0.2386 -- 100.0
X Ray Diffraction 3.7042 4.0767 2716 135 2581 0.1562 0.2164 -- 100.0
X Ray Diffraction 4.0767 4.666 2731 137 2594 0.1368 0.171 -- 100.0
X Ray Diffraction 4.666 5.8764 2752 138 2614 0.1531 0.1977 -- 100.0
X Ray Diffraction 5.8764 43.5371 2876 144 2732 0.1515 0.1974 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 46.5757
Anisotropic B[1][1] 6.008
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 7.7252
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -13.7332
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.187
f_plane_restr 0.005
f_chiral_restr 0.071
f_angle_d 1.066
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7676
Nucleic Acid Atoms 0
Heterogen Atoms 106
Solvent Atoms 205

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: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction