2JI6

X-ray structure of Oxalyl-CoA decarboxylase in complex with 3-deaza- ThDP and oxalyl-CoA


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.958

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.002α = 90
b = 127.002β = 90
c = 151.813γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHVERTICALLY FOCUSING CYLINDRICAL MIRROR2006-03-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I711MAX III711

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
12.0615296.20.111.868485024.88
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)
12.062.1774.20.52.54.4

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 2C312.063080775399498.50.1760.1740.212RANDOM25.33
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]
2.911.462.91-4.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.669
r_dihedral_angle_4_deg15.752
r_dihedral_angle_3_deg13.939
r_dihedral_angle_1_deg5.761
r_scangle_it1.897
r_scbond_it1.486
r_angle_refined_deg1.388
r_mcangle_it1.323
r_mcbond_it1.107
r_angle_other_deg0.905
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.669
r_dihedral_angle_4_deg15.752
r_dihedral_angle_3_deg13.939
r_dihedral_angle_1_deg5.761
r_scangle_it1.897
r_scbond_it1.486
r_angle_refined_deg1.388
r_mcangle_it1.323
r_mcbond_it1.107
r_angle_other_deg0.905
r_symmetry_vdw_other0.248
r_nbd_refined0.192
r_nbd_other0.184
r_nbtor_refined0.168
r_xyhbond_nbd_refined0.157
r_symmetry_hbond_refined0.141
r_symmetry_vdw_refined0.128
r_chiral_restr0.119
r_nbtor_other0.085
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d0.001
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 Atoms908
Heterogen Atoms272

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing