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Crystal structure of Biotin carboxylase from E. coli in complex with the imidazole-pyrimidine inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J9G PDB ENTRY 2J9G
Crystallization Crystal Properties Matthews coefficient Solvent content 2.63 52.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.664 α = 90 b = 113.74 β = 90 c = 121.786 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 ADSC CCD 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 1.99 80 98.1 0.06 23.34 4.47 75853
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 1.99 2.06 92.1 0.54 2.63 4.3
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 1.99 83.05 72012 3807 98.2 0.195 0.194 0.1957 0.229 RANDOM 28.16
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] 0.37 0.07 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.406 r_dihedral_angle_4_deg 17.243 r_dihedral_angle_3_deg 13.701 r_dihedral_angle_1_deg 4.985 r_scangle_it 2.254 r_scbond_it 1.353 r_angle_refined_deg 1.042 r_mcangle_it 0.827 r_mcbond_it 0.486 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.406 r_dihedral_angle_4_deg 17.243 r_dihedral_angle_3_deg 13.701 r_dihedral_angle_1_deg 4.985 r_scangle_it 2.254 r_scbond_it 1.353 r_angle_refined_deg 1.042 r_mcangle_it 0.827 r_mcbond_it 0.486 r_nbtor_refined 0.294 r_symmetry_vdw_refined 0.196 r_nbd_refined 0.178 r_xyhbond_nbd_refined 0.12 r_symmetry_hbond_refined 0.114 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 6868 Nucleic Acid Atoms Solvent Atoms 671 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing