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Crystal structure of biotin carboxylase from S. aureus complexed with AMPPNP
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 0.2M KCL; 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.29 45.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.247 α = 90 b = 63.318 β = 103.82 c = 105.142 γ = 90
Symmetry Space Group P 1 21 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 2007-08-13 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 2.1 50 93.8 0.14 8.07 3.2 55214
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 2.1 2.18 70.1 0.43 1.9 2.3
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 1DV2 2.1 20 52269 2810 94.1 0.219 0.215 0.2197 0.284 RANDOM 19.18
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] 0.35 -0.21 -1.68 1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.811 r_dihedral_angle_3_deg 16.201 r_dihedral_angle_4_deg 15.623 r_dihedral_angle_1_deg 6.009 r_scangle_it 1.79 r_angle_refined_deg 1.231 r_scbond_it 1.181 r_angle_other_deg 0.885 r_mcangle_it 0.707 r_mcbond_it 0.608
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.811 r_dihedral_angle_3_deg 16.201 r_dihedral_angle_4_deg 15.623 r_dihedral_angle_1_deg 6.009 r_scangle_it 1.79 r_angle_refined_deg 1.231 r_scbond_it 1.181 r_angle_other_deg 0.885 r_mcangle_it 0.707 r_mcbond_it 0.608 r_symmetry_vdw_other 0.246 r_symmetry_vdw_refined 0.204 r_nbd_refined 0.194 r_nbd_other 0.192 r_xyhbond_nbd_refined 0.182 r_symmetry_hbond_refined 0.175 r_nbtor_refined 0.171 r_nbtor_other 0.084 r_chiral_restr 0.07 r_bond_refined_d 0.009 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 6967 Nucleic Acid Atoms Solvent Atoms 817 Heterogen Atoms 68
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing REFMAC phasing REFMAC refinement