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Crystal structure of capreomycin phosphotransferase in complex with CMN IIB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7F0A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 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 3.93 68.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.101 α = 90 b = 92.101 β = 90 c = 119.006 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 210 2020-12-17 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 2.1 30 98.5 0.9764 49.02 6.8 30103
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 2.1 2.18 0.897 3.45
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 7F0A 2.1 21.15 27774 2321 98.52 0.1891 0.1863 0.1959 0.2228 0.2274 RANDOM 31.763
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.104 r_dihedral_angle_4_deg 22.809 r_dihedral_angle_3_deg 14.903 r_dihedral_angle_1_deg 7.508 r_angle_refined_deg 1.926 r_angle_other_deg 1.519 r_chiral_restr 0.124 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.104 r_dihedral_angle_4_deg 22.809 r_dihedral_angle_3_deg 14.903 r_dihedral_angle_1_deg 7.508 r_angle_refined_deg 1.926 r_angle_other_deg 1.519 r_chiral_restr 0.124 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2162 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 46
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing