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Crystal structure of Biotin carboxylase from E. coli in complex with 4-Amino-7,7-dimethyl-7,8-dihydro-quinazolinone fragment
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 2.41 48.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.629 α = 90 b = 113.367 β = 90 c = 121.737 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 2.5 100 88.4 0.1 14.45 4.61 29998
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 2.5 2.59 90 0.47 2.93 3.8
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 2.5 15 28116 1520 88.7 0.234 0.23 0.2232 0.308 RANDOM 32.81
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] 3.66 -1.44 -2.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.686 r_dihedral_angle_4_deg 16.756 r_dihedral_angle_3_deg 16.751 r_dihedral_angle_1_deg 5.453 r_scangle_it 1.838 r_angle_refined_deg 1.132 r_scbond_it 1.106 r_mcangle_it 0.826 r_mcbond_it 0.466 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.686 r_dihedral_angle_4_deg 16.756 r_dihedral_angle_3_deg 16.751 r_dihedral_angle_1_deg 5.453 r_scangle_it 1.838 r_angle_refined_deg 1.132 r_scbond_it 1.106 r_mcangle_it 0.826 r_mcbond_it 0.466 r_nbtor_refined 0.299 r_symmetry_hbond_refined 0.245 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.17 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.078 r_bond_refined_d 0.009 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 6858 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing