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 2 mM CoA, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.28 α = 90
b = 109.67 β = 90
c = 120.07 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 225 mm CCD -- 2011-07-23
Diffraction Radiation
Monochromator Protocol
C(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F

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
1.81 50 100.0 0.083 0.083 -- 11.9 81762 81672 -- -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)
1.81 1.84 100.0 0.482 0.482 5.9 11.7 4005

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 1.809 34.69 -- 0.0 -- 81593 4077 99.76 -- 0.1826 0.1804 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 1.8085 1.8298 2592 128 2464 0.2404 0.2955 -- 94.0
X Ray Diffraction 1.8298 1.8521 2786 139 2647 0.2322 0.2802 -- 100.0
X Ray Diffraction 1.8521 1.8755 2796 140 2656 0.221 0.2917 -- 100.0
X Ray Diffraction 1.8755 1.9002 2764 137 2627 0.216 0.2988 -- 100.0
X Ray Diffraction 1.9002 1.9263 2785 140 2645 0.206 0.2831 -- 100.0
X Ray Diffraction 1.9263 1.9538 2798 140 2658 0.2011 0.2501 -- 100.0
X Ray Diffraction 1.9538 1.9829 2793 140 2653 0.1936 0.266 -- 100.0
X Ray Diffraction 1.9829 2.0139 2780 139 2641 0.1952 0.2746 -- 100.0
X Ray Diffraction 2.0139 2.0469 2801 139 2662 0.2011 0.2471 -- 100.0
X Ray Diffraction 2.0469 2.0822 2771 139 2632 0.1975 0.2744 -- 100.0
X Ray Diffraction 2.0822 2.1201 2802 140 2662 0.1913 0.2537 -- 100.0
X Ray Diffraction 2.1201 2.1608 2786 139 2647 0.1809 0.227 -- 100.0
X Ray Diffraction 2.1608 2.2049 2793 139 2654 0.19 0.2606 -- 100.0
X Ray Diffraction 2.2049 2.2529 2835 142 2693 0.195 0.2503 -- 100.0
X Ray Diffraction 2.2529 2.3053 2782 140 2642 0.1858 0.2646 -- 100.0
X Ray Diffraction 2.3053 2.3629 2794 139 2655 0.1923 0.2394 -- 100.0
X Ray Diffraction 2.3629 2.4268 2829 142 2687 0.1775 0.2253 -- 100.0
X Ray Diffraction 2.4268 2.4982 2829 141 2688 0.177 0.2112 -- 100.0
X Ray Diffraction 2.4982 2.5788 2799 140 2659 0.1724 0.2166 -- 100.0
X Ray Diffraction 2.5788 2.6709 2834 141 2693 0.1825 0.2238 -- 100.0
X Ray Diffraction 2.6709 2.7778 2799 140 2659 0.1872 0.2277 -- 100.0
X Ray Diffraction 2.7778 2.9042 2826 142 2684 0.1806 0.224 -- 100.0
X Ray Diffraction 2.9042 3.0572 2864 143 2721 0.1899 0.2565 -- 100.0
X Ray Diffraction 3.0572 3.2486 2813 141 2672 0.186 0.2156 -- 100.0
X Ray Diffraction 3.2486 3.4992 2839 141 2698 0.1695 0.1899 -- 100.0
X Ray Diffraction 3.4992 3.851 2861 143 2718 0.1606 0.2081 -- 100.0
X Ray Diffraction 3.851 4.4073 2892 145 2747 0.15 0.1887 -- 100.0
X Ray Diffraction 4.4073 5.549 2910 146 2764 0.1547 0.1938 -- 100.0
X Ray Diffraction 5.549 34.696 3040 152 2888 0.1771 0.1777 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.8142
Anisotropic B[1][1] 2.2692
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.5243
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.7934
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.08
f_plane_restr 0.005
f_chiral_restr 0.073
f_angle_d 1.111
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7682
Nucleic Acid Atoms 0
Heterogen Atoms 100
Solvent Atoms 689

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: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction