2JI7

X-ray structure of Oxalyl-CoA decarboxylase with covalent reaction intermediate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C31PDB ENTRY 2C31

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.957.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.181α = 90
b = 126.181β = 90
c = 151.938γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL MIRROR2006-09-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.827699.20.0910.23.712418418.66
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.821.9299.90.4823.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2C311.8230118269583199.10.1510.150.176RANDOM19.91
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]
1.170.591.17-1.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.749
r_dihedral_angle_4_deg16.262
r_dihedral_angle_3_deg12.422
r_dihedral_angle_1_deg5.641
r_scangle_it1.824
r_angle_other_deg1.622
r_angle_refined_deg1.425
r_scbond_it1.222
r_mcangle_it1.086
r_mcbond_it0.804
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.749
r_dihedral_angle_4_deg16.262
r_dihedral_angle_3_deg12.422
r_dihedral_angle_1_deg5.641
r_scangle_it1.824
r_angle_other_deg1.622
r_angle_refined_deg1.425
r_scbond_it1.222
r_mcangle_it1.086
r_mcbond_it0.804
r_symmetry_vdw_other0.27
r_nbd_refined0.2
r_nbd_other0.181
r_nbtor_refined0.167
r_symmetry_hbond_refined0.162
r_chiral_restr0.138
r_symmetry_vdw_refined0.135
r_xyhbond_nbd_refined0.118
r_nbtor_other0.085
r_bond_other_d0.01
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8348
Nucleic Acid Atoms
Solvent Atoms1185
Heterogen Atoms342

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing