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1.55 A X-ray crystallographic structure of SapH from Streptomyces sp. (HPH0547) involved in Pseudouridimycin biosynthesis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GHG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1M BTP pH 7.5
0.2M Na-K-Phosphate
27.5% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.2 43.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.581 α = 90 b = 63.191 β = 90 c = 211.415 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 110 PIXEL DECTRIS EIGER X 16M KB mirrors 2020-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.97625 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.55 44.47 98.8 0.079 0.046 0.997 11.1 6.4 121033 1.5 1.5 15.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 88.7 0.598 0.509 0.679 1.5
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 5GHG 1.55 44.47 114927 5991 98.71 0.1606 0.1595 0.1725 0.1823 0.1926 RANDOM 23.519
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] 0.15 0.85 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.915 r_dihedral_angle_4_deg 14.069 r_dihedral_angle_3_deg 12.082 r_dihedral_angle_1_deg 5.717 r_angle_refined_deg 1.421 r_angle_other_deg 0.957 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.915 r_dihedral_angle_4_deg 14.069 r_dihedral_angle_3_deg 12.082 r_dihedral_angle_1_deg 5.717 r_angle_refined_deg 1.421 r_angle_other_deg 0.957 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6275 Nucleic Acid Atoms Solvent Atoms 894 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing