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Crystal Structure of Biotin Carboxylase from Pseudomonas aeruginosa in apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DV1 PDB ENTRY 1DV1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1M TRIS (PH 7.0); 0.2M MGCL2; 17-21% PEG3350
Crystal Properties Matthews coefficient Solvent content 5.37 76.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.402 α = 90 b = 160.402 β = 90 c = 146.764 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 2006-08-01 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 20 100 0.07 33.6 7.4 75554
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 2.59 100 0.37 4.7 7.3
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 1DV1 2.5 46.13 71168 3769 99.2 0.198 0.196 0.1856 0.223 RANDOM 32.56
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] 0.52 0.26 0.52 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.593 r_dihedral_angle_4_deg 17.158 r_dihedral_angle_3_deg 13.867 r_dihedral_angle_1_deg 5.811 r_scangle_it 1.8 r_scbond_it 1.195 r_angle_refined_deg 1.083 r_angle_other_deg 0.842 r_mcangle_it 0.786 r_mcbond_it 0.723
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.593 r_dihedral_angle_4_deg 17.158 r_dihedral_angle_3_deg 13.867 r_dihedral_angle_1_deg 5.811 r_scangle_it 1.8 r_scbond_it 1.195 r_angle_refined_deg 1.083 r_angle_other_deg 0.842 r_mcangle_it 0.786 r_mcbond_it 0.723 r_symmetry_vdw_other 0.224 r_nbd_refined 0.199 r_nbd_other 0.19 r_nbtor_refined 0.168 r_symmetry_hbond_refined 0.152 r_xyhbond_nbd_refined 0.12 r_symmetry_vdw_refined 0.091 r_nbtor_other 0.081 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 6731 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing