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 succinyl-CoA, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.4 α = 90
b = 110.28 β = 90
c = 120.24 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
1.97 50 100.0 0.12 0.12 -- 14.2 63807 63807 -- -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)
1.97 2.0 99.9 0.491 0.491 6.3 13.4 3167

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 1.973 40.22 -- 0.0 -- 63732 3179 99.84 -- 0.1569 0.1542 0.2089 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 1.9726 2.002 2654 130 2524 0.1816 0.2636 -- 97.0
X Ray Diffraction 2.002 2.0333 2728 137 2591 0.1707 0.2277 -- 100.0
X Ray Diffraction 2.0333 2.0666 2717 123 2594 0.1788 0.2483 -- 100.0
X Ray Diffraction 2.0666 2.1023 2754 148 2606 0.1782 0.2713 -- 100.0
X Ray Diffraction 2.1023 2.1405 2722 128 2594 0.1665 0.2703 -- 100.0
X Ray Diffraction 2.1405 2.1817 2788 136 2652 0.1605 0.2383 -- 100.0
X Ray Diffraction 2.1817 2.2262 2736 143 2593 0.1655 0.2472 -- 100.0
X Ray Diffraction 2.2262 2.2746 2726 149 2577 0.1753 0.2418 -- 100.0
X Ray Diffraction 2.2746 2.3275 2763 145 2618 0.1709 0.2608 -- 100.0
X Ray Diffraction 2.3275 2.3857 2731 130 2601 0.1681 0.2531 -- 100.0
X Ray Diffraction 2.3857 2.4502 2777 127 2650 0.1629 0.2156 -- 100.0
X Ray Diffraction 2.4502 2.5223 2754 146 2608 0.1589 0.2067 -- 100.0
X Ray Diffraction 2.5223 2.6037 2758 145 2613 0.1565 0.1981 -- 100.0
X Ray Diffraction 2.6037 2.6967 2756 131 2625 0.1654 0.2282 -- 100.0
X Ray Diffraction 2.6967 2.8047 2769 134 2635 0.176 0.2515 -- 100.0
X Ray Diffraction 2.8047 2.9323 2779 142 2637 0.1646 0.2105 -- 100.0
X Ray Diffraction 2.9323 3.0868 2768 125 2643 0.1683 0.2331 -- 100.0
X Ray Diffraction 3.0868 3.2801 2783 152 2631 0.1547 0.2009 -- 100.0
X Ray Diffraction 3.2801 3.5332 2805 132 2673 0.1469 0.1796 -- 100.0
X Ray Diffraction 3.5332 3.8886 2793 145 2648 0.1336 0.1843 -- 100.0
X Ray Diffraction 3.8886 4.4506 2832 138 2694 0.1256 0.1562 -- 100.0
X Ray Diffraction 4.4506 5.6049 2856 146 2710 0.1263 0.1704 -- 100.0
X Ray Diffraction 5.6049 40.2281 2983 147 2836 0.14 0.171 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.5026
Anisotropic B[1][1] 4.7659
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.08
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.6859
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.272
f_plane_restr 0.005
f_chiral_restr 0.07
f_angle_d 1.067
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7676
Nucleic Acid Atoms 0
Heterogen Atoms 100
Solvent Atoms 795

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