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Flavophos biosynthetic enzyme BsfD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C6C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 287 1.6 M lithium sulfate
100 mM Tris HCl, pH=8.5
Crystal Properties Matthews coefficient Solvent content 3.03 59.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.469 α = 90 b = 120.238 β = 90 c = 121.458 γ = 90
Symmetry Space Group I 2 2 2
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 R 4M 2020-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.72 85.5 97.8 0.072 0.076 0.998 23.3 14.1 42079
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.746 1.038 1.089 0.763 2.1
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 1.72 25 39765 2052 99.51 0.18229 0.18139 0.183 0.19927 0.2031 RANDOM 27.068
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] 0.57 0.59 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.667 r_dihedral_angle_1_deg 6.374 r_long_range_B_refined 5.349 r_dihedral_angle_2_deg 3.64 r_scbond_it 1.764 r_mcangle_it 1.617 r_angle_refined_deg 1.06 r_mcbond_it 0.941 r_chiral_restr 0.086 r_bond_refined_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.667 r_dihedral_angle_1_deg 6.374 r_long_range_B_refined 5.349 r_dihedral_angle_2_deg 3.64 r_scbond_it 1.764 r_mcangle_it 1.617 r_angle_refined_deg 1.06 r_mcbond_it 0.941 r_chiral_restr 0.086 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 2231 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction