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Crystal structure of Biotin carboxylase from E. coli in complex with the 3-(3-Methyl-but-2-enyl)-3H-purin-6-ylamine fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J9G PDB ENTRY 2J9G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1M KCL AND 2-8% PEG 800
Crystal Properties Matthews coefficient Solvent content 2.66 53.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.482 α = 90 b = 106.895 β = 90 c = 122.413 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 1.9 80 77.4 0.06 29.58 5.82 67879
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 1.9 1.97 81.2 0.35 4.76 5.6
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 1.9 20 64336 3407 77.2 0.186 0.185 0.1942 0.22 RANDOM 23.48
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] -0.61 0.86 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.023 r_dihedral_angle_4_deg 18.015 r_dihedral_angle_3_deg 13.363 r_dihedral_angle_1_deg 4.911 r_scangle_it 1.974 r_scbond_it 1.332 r_angle_other_deg 1.215 r_angle_refined_deg 1.109 r_mcangle_it 0.784 r_mcbond_it 0.715
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.023 r_dihedral_angle_4_deg 18.015 r_dihedral_angle_3_deg 13.363 r_dihedral_angle_1_deg 4.911 r_scangle_it 1.974 r_scbond_it 1.332 r_angle_other_deg 1.215 r_angle_refined_deg 1.109 r_mcangle_it 0.784 r_mcbond_it 0.715 r_symmetry_vdw_other 0.238 r_nbd_refined 0.19 r_nbd_other 0.178 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.113 r_symmetry_hbond_refined 0.092 r_chiral_restr 0.087 r_symmetry_vdw_refined 0.083 r_nbtor_other 0.081 r_bond_refined_d 0.007 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 6860 Nucleic Acid Atoms Solvent Atoms 510 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing