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Crystal structure of Biotin carboxylase from E. coli in complex with amino-oxazole fragment series
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J9G PDB ENTRY 2J9G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M KCL AND 2-8% PEG-800
Crystal Properties Matthews coefficient Solvent content 2.45 49.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.14 α = 90 b = 105.937 β = 90 c = 122.454 γ = 90
Symmetry Space Group P 21 21 21
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 ASCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID APS 17-ID
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 1.87 20 95.2 0.05 39.97 5.7 86865
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 1.87 1.94 68.2 0.32 5.33 2.9
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2J9G 1.87 80.06 81799 4303 95 0.177 0.175 0.1886 0.217 RANDOM 18.64
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] -0.06 0.35 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.915 r_dihedral_angle_4_deg 18.344 r_dihedral_angle_3_deg 12.93 r_dihedral_angle_1_deg 5.263 r_scangle_it 2.323 r_scbond_it 1.554 r_angle_refined_deg 1.224 r_mcangle_it 0.825 r_angle_other_deg 0.777 r_mcbond_it 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.915 r_dihedral_angle_4_deg 18.344 r_dihedral_angle_3_deg 12.93 r_dihedral_angle_1_deg 5.263 r_scangle_it 2.323 r_scbond_it 1.554 r_angle_refined_deg 1.224 r_mcangle_it 0.825 r_angle_other_deg 0.777 r_mcbond_it 0.75 r_symmetry_vdw_other 0.198 r_nbd_refined 0.193 r_nbd_other 0.177 r_nbtor_refined 0.169 r_symmetry_hbond_refined 0.152 r_xyhbond_nbd_refined 0.144 r_symmetry_vdw_refined 0.112 r_nbtor_other 0.079 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 6850 Nucleic Acid Atoms Solvent Atoms 1061 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing