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X-ray structure of Oxalyl-CoA decarboxylase with covalent reaction intermediate
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 57.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.181 α = 90 b = 126.181 β = 90 c = 151.938 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 ADSC CCD TOROIDAL MIRROR 2006-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.82 76 99.2 0.09 10.2 3.7 124184 18.66
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 1.82 1.92 99.9 0.48 2 3.7
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 1.82 30 118269 5831 99.1 0.151 0.15 0.1577 0.176 0.1825 RANDOM 19.91
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] 1.17 0.59 1.17 -1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.749 r_dihedral_angle_4_deg 16.262 r_dihedral_angle_3_deg 12.422 r_dihedral_angle_1_deg 5.641 r_scangle_it 1.824 r_angle_other_deg 1.622 r_angle_refined_deg 1.425 r_scbond_it 1.222 r_mcangle_it 1.086 r_mcbond_it 0.804
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.749 r_dihedral_angle_4_deg 16.262 r_dihedral_angle_3_deg 12.422 r_dihedral_angle_1_deg 5.641 r_scangle_it 1.824 r_angle_other_deg 1.622 r_angle_refined_deg 1.425 r_scbond_it 1.222 r_mcangle_it 1.086 r_mcbond_it 0.804 r_symmetry_vdw_other 0.27 r_nbd_refined 0.2 r_nbd_other 0.181 r_nbtor_refined 0.167 r_symmetry_hbond_refined 0.162 r_chiral_restr 0.138 r_symmetry_vdw_refined 0.135 r_xyhbond_nbd_refined 0.118 r_nbtor_other 0.085 r_bond_other_d 0.01 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 1185 Heterogen Atoms 342
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing