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Crystal structure of Biotin carboxylase from E. coli in complex with ATP analog, ADPCF2P.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DV2 PDB ENTRY 1DV2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1M KCL, 3-8% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.78 55.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.129 α = 90 b = 106.784 β = 90 c = 121.91 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 2007-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R
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 2.6 20 96 0.1 17.83 3.8 32843
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 2.6 2.69 96.7 0.54 3.3 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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1DV2 2.6 20 31155 1668 95.5 0.192 0.189 0.247 RANDOM 38.83
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] -0.96 2.37 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.653 r_dihedral_angle_4_deg 17.388 r_dihedral_angle_3_deg 15.294 r_dihedral_angle_1_deg 5.334 r_scangle_it 1.391 r_angle_refined_deg 1.111 r_scbond_it 0.895 r_angle_other_deg 0.741 r_mcangle_it 0.565 r_mcbond_it 0.509
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.653 r_dihedral_angle_4_deg 17.388 r_dihedral_angle_3_deg 15.294 r_dihedral_angle_1_deg 5.334 r_scangle_it 1.391 r_angle_refined_deg 1.111 r_scbond_it 0.895 r_angle_other_deg 0.741 r_mcangle_it 0.565 r_mcbond_it 0.509 r_nbd_refined 0.19 r_nbd_other 0.172 r_nbtor_refined 0.172 r_symmetry_vdw_other 0.163 r_xyhbond_nbd_refined 0.138 r_symmetry_vdw_refined 0.122 r_nbtor_other 0.078 r_symmetry_hbond_refined 0.074 r_chiral_restr 0.062 r_bond_refined_d 0.009 r_bond_other_d 0.003 r_gen_planes_refined 0.003 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 6755 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement SCALEPACK data reduction SCALEPACK data scaling MOLREP phasing