2JI9

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.9658.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.721α = 90
b = 127.721β = 90
c = 152.417γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL MIRROR2006-03-10MSINGLE 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
12.263.8997.80.1414.510.77171635
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)
12.22.3287.80.432.46.4

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 2C312.23068216341397.80.1790.1770.215RANDOM31.53
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]
3.31.653.3-4.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.273
r_dihedral_angle_4_deg17.46
r_dihedral_angle_3_deg14.342
r_dihedral_angle_1_deg5.568
r_scangle_it1.631
r_angle_refined_deg1.264
r_scbond_it1.246
r_mcangle_it1.226
r_mcbond_it1.018
r_angle_other_deg0.889
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.273
r_dihedral_angle_4_deg17.46
r_dihedral_angle_3_deg14.342
r_dihedral_angle_1_deg5.568
r_scangle_it1.631
r_angle_refined_deg1.264
r_scbond_it1.246
r_mcangle_it1.226
r_mcbond_it1.018
r_angle_other_deg0.889
r_symmetry_vdw_other0.267
r_nbd_refined0.187
r_nbd_other0.179
r_nbtor_refined0.166
r_symmetry_vdw_refined0.15
r_xyhbond_nbd_refined0.142
r_symmetry_hbond_refined0.126
r_chiral_restr0.094
r_nbtor_other0.084
r_bond_refined_d0.008
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 Atoms8168
Nucleic Acid Atoms
Solvent Atoms616
Heterogen Atoms146

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing