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Crystal structure of mutant-K146A of peptidyl-tRNA hydrolase from Vibrio cholerae at 1.63A resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZXP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 296 100mM Sodium citrate (pH 8), 200mM Ammonium acetate, 20% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.39 48.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.934 α = 90 b = 74.295 β = 90 c = 123.571 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 IMAGE PLATE RIGAKU RAXIS IV++ 2015-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.63 50 88.4 32.1 5.6 46655
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 4ZXP 1.63 50 44043 2345 88.01 0.18914 0.18711 0.1997 0.2281 0.2294 RANDOM 29.066
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] -0.31 1.23 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.616 r_dihedral_angle_4_deg 16.076 r_dihedral_angle_3_deg 13.133 r_long_range_B_refined 7.645 r_long_range_B_other 7.637 r_dihedral_angle_1_deg 6.734 r_scangle_other 4.998 r_scbond_it 3.581 r_scbond_other 3.571 r_mcangle_it 2.951
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.616 r_dihedral_angle_4_deg 16.076 r_dihedral_angle_3_deg 13.133 r_long_range_B_refined 7.645 r_long_range_B_other 7.637 r_dihedral_angle_1_deg 6.734 r_scangle_other 4.998 r_scbond_it 3.581 r_scbond_other 3.571 r_mcangle_it 2.951 r_mcangle_other 2.95 r_mcbond_it 2.157 r_mcbond_other 2.152 r_angle_refined_deg 1.97 r_angle_other_deg 1.652 r_chiral_restr 0.115 r_bond_refined_d 0.018 r_gen_planes_refined 0.012 r_bond_other_d 0.01 r_gen_planes_other 0.007 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3034 Nucleic Acid Atoms Solvent Atoms 383 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling HKL-2000 phasing