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Crystal structure of capreomycin phosphotransferase in complex with CMN IIA
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 3.96 68.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.355 α = 90 b = 92.355 β = 90 c = 119.164 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 2.07 30 99.9 0.9765 58.4 9.6 32042
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 2.07 2.14 0.888 3.66
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7F0A 2.07 25.06 30436 1585 99.79 0.2191 0.2174 0.2537 0.2348 RANDOM 32.13
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] -0.19 -0.19 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.905 r_dihedral_angle_4_deg 14.191 r_dihedral_angle_3_deg 13.973 r_dihedral_angle_1_deg 6.974 r_angle_refined_deg 1.413 r_angle_other_deg 1.291 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.905 r_dihedral_angle_4_deg 14.191 r_dihedral_angle_3_deg 13.973 r_dihedral_angle_1_deg 6.974 r_angle_refined_deg 1.413 r_angle_other_deg 1.291 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2154 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing