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Crystal Structure of E. coli Biotin Carboxylase Complexed with 7-[3-(aminomethyl)pyrrolidin-1-yl]-6-(2,6-dichlorophenyl)pyrido[2,3-d]pyrimidin-2-amine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DV1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1 M HEPES, 30% PEG1000
Crystal Properties Matthews coefficient Solvent content 2.83 56.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.352 α = 90 b = 106.782 β = 90 c = 122.345 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 QUANTUM 315 KB mirrors 2015-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.06 61.25 99.4 0.056 12.8 3.6 68531 13.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.06 2.11 99 0.634 3.7
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1DV1 2.06 61.25 65059 3382 99.26 0.19594 0.19457 0.22292 0.2055 RANDOM 28.66
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] -0.44 0.29 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.93 r_dihedral_angle_4_deg 17.724 r_dihedral_angle_3_deg 14.425 r_dihedral_angle_1_deg 6.456 r_long_range_B_refined 3.799 r_long_range_B_other 3.799 r_angle_refined_deg 1.486 r_angle_other_deg 1.352 r_scangle_other 1.321 r_mcangle_it 1.032
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.93 r_dihedral_angle_4_deg 17.724 r_dihedral_angle_3_deg 14.425 r_dihedral_angle_1_deg 6.456 r_long_range_B_refined 3.799 r_long_range_B_other 3.799 r_angle_refined_deg 1.486 r_angle_other_deg 1.352 r_scangle_other 1.321 r_mcangle_it 1.032 r_mcangle_other 1.032 r_scbond_it 0.818 r_scbond_other 0.818 r_mcbond_it 0.611 r_mcbond_other 0.611 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6868 Nucleic Acid Atoms Solvent Atoms 432 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement xia2 data reduction SCALA data scaling PHASER phasing