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Crystal structure of Peptidyl-tRNA hydrolase mutant -N118D from Vibrio cholerae at 1.63A resolution.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 100mM Soduim citrate, 200mM Ammonium acetate, 25% Polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 2.25 45.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.112 α = 90 b = 71.124 β = 90 c = 124.03 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++ 2014-12-29 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 1.63 62.01 98.9 51.92 6.1 49251
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 1.63 1.69 95.7 4.68 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.63 50 46686 2483 98.89 0.17201 0.17019 0.1851 0.2069 0.1879 RANDOM 26.187
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] 0.15 1.21 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.461 r_dihedral_angle_4_deg 20.557 r_dihedral_angle_3_deg 14.294 r_dihedral_angle_1_deg 7.407 r_long_range_B_refined 6.801 r_long_range_B_other 6.72 r_scangle_other 5.468 r_scbond_it 3.759 r_scbond_other 3.757 r_mcangle_it 3.419
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.461 r_dihedral_angle_4_deg 20.557 r_dihedral_angle_3_deg 14.294 r_dihedral_angle_1_deg 7.407 r_long_range_B_refined 6.801 r_long_range_B_other 6.72 r_scangle_other 5.468 r_scbond_it 3.759 r_scbond_other 3.757 r_mcangle_it 3.419 r_mcangle_other 3.419 r_mcbond_it 2.43 r_mcbond_other 2.429 r_angle_refined_deg 2.08 r_angle_other_deg 0.922 r_chiral_restr 0.124 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_bond_other_d 0.002 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 3008 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling HKL-2000 phasing