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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 Crystal Properties Matthews coefficient Solvent content 2.52 50.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.242 α = 90 b = 106.197 β = 90 c = 122.277 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 2 20 99.9 0.08 25.23 6.82 74778
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 2.07 99.7 0.5 4.47 6.7
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2J9G 2 80.06 70942 3766 99.8 0.185 0.183 0.1896 0.208 RANDOM 24.87
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] -0.42 0.92 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.862 r_dihedral_angle_4_deg 16.439 r_dihedral_angle_3_deg 12.967 r_dihedral_angle_1_deg 4.812 r_scangle_it 1.625 r_angle_refined_deg 0.995 r_scbond_it 0.964 r_mcangle_it 0.582 r_mcbond_it 0.343 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.862 r_dihedral_angle_4_deg 16.439 r_dihedral_angle_3_deg 12.967 r_dihedral_angle_1_deg 4.812 r_scangle_it 1.625 r_angle_refined_deg 0.995 r_scbond_it 0.964 r_mcangle_it 0.582 r_mcbond_it 0.343 r_nbtor_refined 0.293 r_symmetry_vdw_refined 0.186 r_nbd_refined 0.171 r_symmetry_hbond_refined 0.112 r_xyhbond_nbd_refined 0.1 r_chiral_restr 0.068 r_bond_refined_d 0.007 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 6860 Nucleic Acid Atoms Solvent Atoms 810 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing