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Flavophos biosynthetic protein BsfD with CoA and OBPn (48 h)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9ZSC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 287 28% PEG 4000
100 mM calcium acetate
100 mM sodium acetate (pH=4.5)
Crystal Properties Matthews coefficient Solvent content 2.68 54.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.924 α = 90 b = 109.684 β = 90 c = 72.521 γ = 90
Symmetry Space Group P 21 21 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 2021-09-24 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 1.806 34.428 100 0.099 0.106 0.999 8.82 14.5 64356
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 1.806 1.837 1.242 1.296 0.779
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 1.81 25 60654 3222 99.94 0.18185 0.18075 0.1837 0.20284 0.2036 RANDOM 26.758
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] 0.26 -0.85 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.267 r_dihedral_angle_1_deg 6.165 r_long_range_B_refined 5.329 r_dihedral_angle_2_deg 2.902 r_scbond_it 1.753 r_mcangle_it 1.561 r_angle_refined_deg 1.108 r_mcbond_it 0.937 r_chiral_restr 0.088 r_bond_refined_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.267 r_dihedral_angle_1_deg 6.165 r_long_range_B_refined 5.329 r_dihedral_angle_2_deg 2.902 r_scbond_it 1.753 r_mcangle_it 1.561 r_angle_refined_deg 1.108 r_mcbond_it 0.937 r_chiral_restr 0.088 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 4354 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction