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X-ray structure of Oxalyl-CoA decarboxylase in complex with 3-deaza- ThDP and oxalyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C31 PDB ENTRY 2C31
Crystallization Crystal Properties Matthews coefficient Solvent content 2.9 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.002 α = 90 b = 127.002 β = 90 c = 151.813 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH VERTICALLY FOCUSING CYLINDRICAL MIRROR 2006-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 MAX II I711
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.06 152 96.2 0.1 11.8 6 84850 24.88
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.06 2.17 74.2 0.5 2.5 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2C31 2.06 30 80775 3994 98.5 0.176 0.174 0.1779 0.212 0.2154 RANDOM 25.33
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] 2.91 1.46 2.91 -4.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.669 r_dihedral_angle_4_deg 15.752 r_dihedral_angle_3_deg 13.939 r_dihedral_angle_1_deg 5.761 r_scangle_it 1.897 r_scbond_it 1.486 r_angle_refined_deg 1.388 r_mcangle_it 1.323 r_mcbond_it 1.107 r_angle_other_deg 0.905
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.669 r_dihedral_angle_4_deg 15.752 r_dihedral_angle_3_deg 13.939 r_dihedral_angle_1_deg 5.761 r_scangle_it 1.897 r_scbond_it 1.486 r_angle_refined_deg 1.388 r_mcangle_it 1.323 r_mcbond_it 1.107 r_angle_other_deg 0.905 r_symmetry_vdw_other 0.248 r_nbd_refined 0.192 r_nbd_other 0.184 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.157 r_symmetry_hbond_refined 0.141 r_symmetry_vdw_refined 0.128 r_chiral_restr 0.119 r_nbtor_other 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 8348 Nucleic Acid Atoms Solvent Atoms 908 Heterogen Atoms 272
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing