☰ Navigation Tabs
Crystal structure of the Peptidyl-tRNA hydrolase from Vibrio cholerae in the C121 space group at pH 6.5
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 0.1 M Sodium citrate
0.2 Ammonium acetate,
17.5 % Polyethylene glycol 4000
protein concentration 8 mg/ml
Crystal Properties Matthews coefficient Solvent content 2.07 40.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.861 α = 90 b = 44.507 β = 95.97 c = 108.231 γ = 90
Symmetry Space Group C 1 2 1
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++ 2015-08-26 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 2.01 107.7 95.7 32.5 6.3 22748
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 2.01 2.08
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4ZXP 2.01 107.64 21569 1175 95.25 0.1644 0.16116 0.22443 0.2549 RANDOM 39.248
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] -2.08 -0.77 4.15 -1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.273 r_dihedral_angle_4_deg 18.322 r_dihedral_angle_3_deg 14.773 r_dihedral_angle_1_deg 7.116 r_long_range_B_refined 6.276 r_long_range_B_other 6.263 r_scangle_other 4.727 r_mcangle_it 3.375 r_mcangle_other 3.375 r_scbond_other 3.172
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.273 r_dihedral_angle_4_deg 18.322 r_dihedral_angle_3_deg 14.773 r_dihedral_angle_1_deg 7.116 r_long_range_B_refined 6.276 r_long_range_B_other 6.263 r_scangle_other 4.727 r_mcangle_it 3.375 r_mcangle_other 3.375 r_scbond_other 3.172 r_scbond_it 3.171 r_mcbond_it 2.487 r_mcbond_other 2.487 r_angle_refined_deg 1.737 r_angle_other_deg 0.856 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2996 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing