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Crystal structure of Peptidyl-tRNA hydrolase mutant -M71A 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 295 0.1M sodium citrate, 0.2M ammonium acetate, 20% polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 2.52 51.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.709 α = 90 b = 117.491 β = 90 c = 201.618 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++ 2016-06-10 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) R Merge I (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 2.55 100.81 97.3 0.061 26.96 4.7 14447
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.64 0.206
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 2.55 100.81 13681 733 97.21 0.19028 0.18641 0.1921 0.26316 0.2564 RANDOM 38.039
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] 1.67 -2.35 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.79 r_dihedral_angle_4_deg 20.379 r_dihedral_angle_3_deg 15.886 r_dihedral_angle_1_deg 6.591 r_long_range_B_refined 5.759 r_long_range_B_other 5.755 r_scangle_other 4.031 r_mcangle_it 3.554 r_mcangle_other 3.553 r_scbond_it 2.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.79 r_dihedral_angle_4_deg 20.379 r_dihedral_angle_3_deg 15.886 r_dihedral_angle_1_deg 6.591 r_long_range_B_refined 5.759 r_long_range_B_other 5.755 r_scangle_other 4.031 r_mcangle_it 3.554 r_mcangle_other 3.553 r_scbond_it 2.46 r_scbond_other 2.452 r_mcbond_it 2.225 r_mcbond_other 2.225 r_angle_refined_deg 1.448 r_angle_other_deg 0.813 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 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 2941 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing