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 = 67.39 α = 90
b = 110.48 β = 90
c = 119.16 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 -- 2011-07-24
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 1.9075 APS 21-ID-D

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
2.4 50 98.2 0.063 0.063 -- 5.8 34893 34893 -- -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)
2.4 2.49 100.0 0.109 0.109 33.5 5.7 3477

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 2.398 44.636 -- 0.0 -- -- 3330 97.48 -- 0.1551 0.1522 0.2086 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 2.3984 2.4326 2558 149 2409 0.1525 0.2364 -- 93.0
X Ray Diffraction 2.4326 2.4689 2781 173 2608 0.16 0.2404 -- 99.0
X Ray Diffraction 2.4689 2.5075 2785 134 2651 0.1739 0.3017 -- 99.0
X Ray Diffraction 2.5075 2.5486 2810 118 2692 0.1684 0.2407 -- 100.0
X Ray Diffraction 2.5486 2.5925 2806 130 2676 0.1766 0.2709 -- 100.0
X Ray Diffraction 2.5925 2.6397 2789 137 2652 0.1609 0.2615 -- 99.0
X Ray Diffraction 2.6397 2.6905 2802 156 2646 0.1651 0.2463 -- 100.0
X Ray Diffraction 2.6905 2.7454 2755 144 2611 0.1581 0.2205 -- 99.0
X Ray Diffraction 2.7454 2.805 2775 146 2629 0.1658 0.1997 -- 99.0
X Ray Diffraction 2.805 2.8703 2734 134 2600 0.1596 0.24 -- 99.0
X Ray Diffraction 2.8703 2.9421 2837 143 2694 0.1653 0.2343 -- 99.0
X Ray Diffraction 2.9421 3.0216 2719 141 2578 0.1751 0.2664 -- 98.0
X Ray Diffraction 3.0216 3.1105 2755 130 2625 0.1801 0.281 -- 98.0
X Ray Diffraction 3.1105 3.2108 2779 128 2651 0.1717 0.2423 -- 98.0
X Ray Diffraction 3.2108 3.3256 2732 144 2588 0.1574 0.2289 -- 98.0
X Ray Diffraction 3.3256 3.4587 2720 136 2584 0.152 0.2121 -- 97.0
X Ray Diffraction 3.4587 3.616 2729 137 2592 0.1547 0.2078 -- 97.0
X Ray Diffraction 3.616 3.8066 2713 136 2577 0.1431 0.1822 -- 97.0
X Ray Diffraction 3.8066 4.0449 2731 137 2594 0.1281 0.1566 -- 97.0
X Ray Diffraction 4.0449 4.357 2654 149 2505 0.1196 0.1595 -- 96.0
X Ray Diffraction 4.357 4.795 2711 118 2593 0.1122 0.1403 -- 95.0
X Ray Diffraction 4.795 5.4877 2653 140 2513 0.1237 0.1468 -- 96.0
X Ray Diffraction 5.4877 6.9098 2671 130 2541 0.1596 0.1815 -- 95.0
X Ray Diffraction 6.9098 44.6438 2607 140 2467 0.167 0.1777 -- 93.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.2142
Anisotropic B[1][1] -1.5041
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.2349
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.7308
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.148
f_plane_restr 0.005
f_chiral_restr 0.068
f_angle_d 1.023
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7764
Nucleic Acid Atoms 0
Heterogen Atoms 100
Solvent Atoms 500

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