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Crystal structure of capreomycin phosphotransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IGI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.4 M sodium malonate pH 7.0, 0.1 M Bis-Tris propane pH 7.0, 0.1 M calcium chloride dihydrate
Crystal Properties Matthews coefficient Solvent content 4.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.969 α = 90 b = 91.969 β = 90 c = 120.053 γ = 90
Symmetry Space Group P 42 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 80 CCD ADSC QUANTUM 315r 2020-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 0.9732 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.95 30 96.9 0.995 50.6 9.9 37001
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02 0.887 3.56
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 5IGI 1.95 28.61 35206 1795 96.89 0.1917 0.1903 0.1986 0.2182 0.2274 RANDOM 42.332
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] -0.01 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.186 r_dihedral_angle_4_deg 20.01 r_dihedral_angle_3_deg 15.015 r_dihedral_angle_1_deg 7.321 r_angle_refined_deg 1.775 r_angle_other_deg 1.504 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.186 r_dihedral_angle_4_deg 20.01 r_dihedral_angle_3_deg 15.015 r_dihedral_angle_1_deg 7.321 r_angle_refined_deg 1.775 r_angle_other_deg 1.504 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2116 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing