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X-Ray Crystal Structure of the biotin synthase from V. parvula
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other unpublished structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 0.1M Bis-Tris pH 5.5, 0.2M NH4OAc, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.15 42.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.465 α = 90 b = 70.218 β = 90 c = 195.85 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 PIXEL DECTRIS EIGER X 16M mirrors 2018-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9793 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.807 29.6 99.7 0.094 0.102 0.039 0.999 12.6 6.7 60902
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.81 1.85 96 0.757 0.827 0.328 0.855 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.807 29.6 55335 1865 93.72 0.18022 0.17868 0.1876 0.22689 0.2331 RANDOM 27.7
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] 3.37 -1.25 -2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.957 r_dihedral_angle_2_deg 7.06 r_long_range_B_refined 6.623 r_dihedral_angle_1_deg 6.589 r_long_range_B_other 6.393 r_scangle_other 4.945 r_mcangle_it 3.327 r_mcangle_other 3.327 r_scbond_it 3.175 r_scbond_other 3.175
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.957 r_dihedral_angle_2_deg 7.06 r_long_range_B_refined 6.623 r_dihedral_angle_1_deg 6.589 r_long_range_B_other 6.393 r_scangle_other 4.945 r_mcangle_it 3.327 r_mcangle_other 3.327 r_scbond_it 3.175 r_scbond_other 3.175 r_angle_refined_deg 2.432 r_mcbond_it 2.382 r_mcbond_other 2.379 r_angle_other_deg 1.095 r_chiral_restr 0.196 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 5113 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 119
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing