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Crystal structure of Peptidyl-tRNA hydrolase from Vibrio cholerae in space group C2221 at resolution 1.75A.
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 5.6 293 100 mM sodium acetate (pH 5.6), 200 mM potassium sodium tartrate, 2M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.36 47.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.136 α = 90 b = 73.462 β = 90 c = 120.52 γ = 90
Symmetry Space Group C 2 2 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++ 2016-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 1.75 50 99.3 50.1 12.9 20981
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.81
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 1.75 50 19759 1072 98.63 0.1932 0.191 0.2011 0.23499 0.2373 RANDOM 26.978
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] 0.34 -0.35 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.844 r_dihedral_angle_4_deg 19.901 r_dihedral_angle_3_deg 13.958 r_dihedral_angle_1_deg 6.537 r_long_range_B_refined 6.016 r_long_range_B_other 6.015 r_scangle_other 3.981 r_scbond_it 2.635 r_scbond_other 2.634 r_mcangle_it 2.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.844 r_dihedral_angle_4_deg 19.901 r_dihedral_angle_3_deg 13.958 r_dihedral_angle_1_deg 6.537 r_long_range_B_refined 6.016 r_long_range_B_other 6.015 r_scangle_other 3.981 r_scbond_it 2.635 r_scbond_other 2.634 r_mcangle_it 2.302 r_mcangle_other 2.301 r_angle_refined_deg 1.897 r_mcbond_it 1.649 r_mcbond_other 1.606 r_angle_other_deg 0.919 r_chiral_restr 0.11 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 1482 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing