☰ Navigation Tabs
Structural Analysis of Substrate, Reaction Intermediate and Product Binding in Haemophilus influenzae Biotin Carboxylase
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, SITTING DROP 298.15 16% PEG3350
0.2M KCl Protein was incubated with solid N1 -methoxycarbonylbiotin methyl ester for 5 days prior to crystallization, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K
Crystal Properties Matthews coefficient Solvent content 2.14 42.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.197 α = 90 b = 86.197 β = 90 c = 102.364 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 2013-10-31 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) R Sym 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 1.98 39.72 99.9 0.056 19.5 5.6 30073 30073 27.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.09 100 0.504 2.8 5.7 4385
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1DV1 1.98 39.72 28578 28578 1464 99.86 0.17828 0.17828 0.17629 0.1855 0.21697 0.2211 RANDOM 44.666
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] -0.11 -0.05 -0.11 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.753 r_dihedral_angle_3_deg 17.197 r_dihedral_angle_4_deg 14.18 r_dihedral_angle_1_deg 6.797 r_long_range_B_refined 5.601 r_long_range_B_other 5.601 r_scangle_other 3.79 r_scbond_it 2.725 r_scbond_other 2.724 r_mcangle_it 2.468
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.753 r_dihedral_angle_3_deg 17.197 r_dihedral_angle_4_deg 14.18 r_dihedral_angle_1_deg 6.797 r_long_range_B_refined 5.601 r_long_range_B_other 5.601 r_scangle_other 3.79 r_scbond_it 2.725 r_scbond_other 2.724 r_mcangle_it 2.468 r_mcangle_other 2.467 r_angle_refined_deg 2.055 r_mcbond_it 1.688 r_mcbond_other 1.682 r_angle_other_deg 0.913 r_chiral_restr 0.116 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 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 3235 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 48
Software Software Software Name Purpose XDS data scaling MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling