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Crystal Structure of Haemophilus Influenzae Biotin Carboxylase Complexed with (R)-7-(3-aminopyrrolidin-1-yl)-6-(naphthalen-1-yl)pyrido[2,3-d]pyrimidin-2-amine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RZQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.2M Ca acetate, 14% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.19 43.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.688 α = 90 b = 85.688 β = 90 c = 104.83 γ = 120
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 2.05 39.69 99.3 0.035 18.7 3.7 27210
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 2.05 2.11 97.9 0.532 1.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4RZQ 2.05 39.69 25814 1376 99.22 0.17795 0.1756 0.1833 0.22244 0.2288 RANDOM 35.725
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] -0.33 -0.16 -0.33 1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.892 r_dihedral_angle_3_deg 16.384 r_dihedral_angle_4_deg 14.398 r_dihedral_angle_1_deg 6.767 r_long_range_B_refined 4.283 r_long_range_B_other 4.283 r_scangle_other 1.673 r_angle_refined_deg 1.602 r_angle_other_deg 1.335 r_mcangle_it 1.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.892 r_dihedral_angle_3_deg 16.384 r_dihedral_angle_4_deg 14.398 r_dihedral_angle_1_deg 6.767 r_long_range_B_refined 4.283 r_long_range_B_other 4.283 r_scangle_other 1.673 r_angle_refined_deg 1.602 r_angle_other_deg 1.335 r_mcangle_it 1.305 r_mcangle_other 1.301 r_scbond_it 1.074 r_scbond_other 1.074 r_mcbond_it 0.828 r_mcbond_other 0.816 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 3413 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing