2JIB

X-ray structure of Oxalyl-CoA decarboxylase in complex with coenzyme- A


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 = 127.662α = 90
b = 127.662β = 90
c = 152.074γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDSAGITALLY FOCUSING GE(220) AND A MULTILAYER2006-05-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
12.263.8999.20.0810.13.37234127.7
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)
12.22.3299.40.173.83.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2C312.230688213439990.2010.1990.238RANDOM26.6
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]
4.172.094.17-6.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.41
r_dihedral_angle_4_deg16.72
r_dihedral_angle_3_deg14.1
r_dihedral_angle_1_deg5.661
r_angle_refined_deg1.169
r_scangle_it1.072
r_angle_other_deg0.861
r_scbond_it0.742
r_mcangle_it0.393
r_mcbond_it0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.41
r_dihedral_angle_4_deg16.72
r_dihedral_angle_3_deg14.1
r_dihedral_angle_1_deg5.661
r_angle_refined_deg1.169
r_scangle_it1.072
r_angle_other_deg0.861
r_scbond_it0.742
r_mcangle_it0.393
r_mcbond_it0.33
r_symmetry_vdw_other0.241
r_nbd_refined0.188
r_nbd_other0.18
r_nbtor_refined0.166
r_xyhbond_nbd_refined0.144
r_symmetry_vdw_refined0.139
r_symmetry_hbond_refined0.137
r_nbtor_other0.084
r_chiral_restr0.065
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 Atoms8348
Nucleic Acid Atoms
Solvent Atoms666
Heterogen Atoms224

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing