8AFF | pdb_00008aff

Wild type oxalyl-CoA synthetase Pcs60p


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFoldAlphaFold

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82980.2 M LiCl, 0.1M Hepes pH 8.0, 10-16% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4850.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.029α = 90
b = 93.724β = 93.811
c = 356.488γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2016-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.966ESRFMASSIF-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.8729.98599.20.998.61.9163072
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.872.9799.60.51.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEAlphaFold2.8729.985163027818699.0030.2290.22740.230.24970.2580.108
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
1.818-1.017-1.195-0.483
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.454
r_dihedral_angle_4_deg20.115
r_dihedral_angle_3_deg19.637
r_dihedral_angle_1_deg7.651
r_lrange_it5.439
r_mcangle_it2.522
r_scangle_it2.216
r_angle_refined_deg1.75
r_mcbond_it1.46
r_scbond_it1.303
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms42466
Nucleic Acid Atoms
Solvent Atoms317
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing