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Crystal structure of HitB in complex with (S)-beta-3-Br-phenylalanine sulfamoyladenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DQ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG 400, calcium acetate, sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.29 46.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.965 α = 90 b = 96.693 β = 90 c = 166.414 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 PILATUS3 S 6M 2019-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.6 50 99.9 0.089 0.999 17.5 6.6 34560
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.72 100 0.804 0.861 2.5 6.4
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 7DQ5 2.6 48.39 32819 1679 99.92 0.215 0.2121 0.2192 0.2698 0.2715 RANDOM 63.691
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] -1.74 4.12 -2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.415 r_dihedral_angle_4_deg 19.567 r_dihedral_angle_3_deg 18.153 r_dihedral_angle_1_deg 6.99 r_angle_refined_deg 1.517 r_angle_other_deg 1.238 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.415 r_dihedral_angle_4_deg 19.567 r_dihedral_angle_3_deg 18.153 r_dihedral_angle_1_deg 6.99 r_angle_refined_deg 1.517 r_angle_other_deg 1.238 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7026 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing