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Crystal structure of mutant-D97N of peptidyl-tRNA hydrolase from Vibrio cholerae
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 288 100 mM Sodium citrate,
200 mM Ammonium acetate,
20% Polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 2.29 46.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.455 α = 90 b = 71.628 β = 90 c = 123.929 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++ 2015-12-21 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 2.09 50 97.3 19.68 6.6 23401
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 2.1 2.14
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 2.09 35.79 22168 1201 97.17 0.18645 0.18298 0.1922 0.25431 0.2548 RANDOM 36.957
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] 0.77 2.15 -2.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.925 r_dihedral_angle_4_deg 20.118 r_dihedral_angle_3_deg 15.33 r_long_range_B_other 7.667 r_long_range_B_refined 7.663 r_dihedral_angle_1_deg 6.835 r_scangle_other 5.563 r_mcangle_it 4.221 r_mcangle_other 4.221 r_scbond_it 3.644
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.925 r_dihedral_angle_4_deg 20.118 r_dihedral_angle_3_deg 15.33 r_long_range_B_other 7.667 r_long_range_B_refined 7.663 r_dihedral_angle_1_deg 6.835 r_scangle_other 5.563 r_mcangle_it 4.221 r_mcangle_other 4.221 r_scbond_it 3.644 r_scbond_other 3.638 r_mcbond_it 2.914 r_mcbond_other 2.912 r_angle_refined_deg 1.746 r_angle_other_deg 0.857 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 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 2980 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling HKL-2000 phasing