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 = 67.09 α = 90
b = 110.1 β = 90
c = 119.84 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
1.48 50 99.9 0.079 0.079 -- 13.6 148137 148137 -- -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)
1.48 1.51 99.8 0.574 0.574 4.4 12.9 7318

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 1.479 30.998 -- 0.0 -- 147934 7386 99.83 -- 0.1585 0.1574 0.1792 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 1.4795 1.4963 4828 232 4596 0.1914 0.2213 -- 98.0
X Ray Diffraction 1.4963 1.5139 4828 251 4577 0.1887 0.2494 -- 100.0
X Ray Diffraction 1.5139 1.5324 4901 252 4649 0.1783 0.2218 -- 100.0
X Ray Diffraction 1.5324 1.5518 4899 254 4645 0.1711 0.1952 -- 100.0
X Ray Diffraction 1.5518 1.5722 4873 225 4648 0.1678 0.2055 -- 100.0
X Ray Diffraction 1.5722 1.5937 4897 234 4663 0.167 0.1926 -- 100.0
X Ray Diffraction 1.5937 1.6165 4881 248 4633 0.16 0.1977 -- 100.0
X Ray Diffraction 1.6165 1.6406 4901 238 4663 0.1594 0.1997 -- 100.0
X Ray Diffraction 1.6406 1.6662 4869 236 4633 0.1624 0.2008 -- 100.0
X Ray Diffraction 1.6662 1.6936 4946 262 4684 0.1604 0.1952 -- 100.0
X Ray Diffraction 1.6936 1.7228 4871 222 4649 0.1535 0.1757 -- 100.0
X Ray Diffraction 1.7228 1.7541 4877 270 4607 0.158 0.2069 -- 100.0
X Ray Diffraction 1.7541 1.7878 4911 254 4657 0.1579 0.2038 -- 100.0
X Ray Diffraction 1.7878 1.8243 4906 218 4688 0.1629 0.1973 -- 100.0
X Ray Diffraction 1.8243 1.864 4938 257 4681 0.1602 0.1906 -- 100.0
X Ray Diffraction 1.864 1.9073 4897 239 4658 0.1524 0.1688 -- 100.0
X Ray Diffraction 1.9073 1.955 4896 261 4635 0.1572 0.1872 -- 100.0
X Ray Diffraction 1.955 2.0079 4921 236 4685 0.1592 0.1825 -- 100.0
X Ray Diffraction 2.0079 2.0669 4927 253 4674 0.1592 0.1813 -- 100.0
X Ray Diffraction 2.0669 2.1336 4903 231 4672 0.1552 0.1789 -- 100.0
X Ray Diffraction 2.1336 2.2099 4924 258 4666 0.1518 0.1742 -- 100.0
X Ray Diffraction 2.2099 2.2983 4945 245 4700 0.1583 0.1757 -- 100.0
X Ray Diffraction 2.2983 2.4029 4952 252 4700 0.1609 0.1987 -- 100.0
X Ray Diffraction 2.4029 2.5295 4923 240 4683 0.161 0.1897 -- 100.0
X Ray Diffraction 2.5295 2.6879 4985 249 4736 0.1731 0.1934 -- 100.0
X Ray Diffraction 2.6879 2.8953 4984 247 4737 0.1692 0.2075 -- 100.0
X Ray Diffraction 2.8953 3.1864 4997 254 4743 0.1651 0.1868 -- 100.0
X Ray Diffraction 3.1864 3.6469 5017 250 4767 0.1427 0.1366 -- 100.0
X Ray Diffraction 3.6469 4.5923 5073 250 4823 0.1292 0.1386 -- 100.0
X Ray Diffraction 4.5923 31.0047 5264 268 4996 0.1602 0.1622 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.2522
Anisotropic B[1][1] -1.2319
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.8218
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.5899
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.857
f_plane_restr 0.006
f_chiral_restr 0.075
f_angle_d 1.143
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7764
Nucleic Acid Atoms 0
Heterogen Atoms 100
Solvent Atoms 1326

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