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Crystal structure of human prolyl-tRNA synthetase in complex with Aze-SA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HVC PDB entry 4HVC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 293 9% PEG3350, 250 mM sodium nitrate, 100 mM 3-(1-pyridino)-1-propane sulfonate
Crystal Properties Matthews coefficient Solvent content 2.08 40.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.766 α = 90 b = 86.766 β = 90 c = 108.773 γ = 120
Symmetry Space Group P 32 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 MAR scanner 345 mm plate 2012-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.59 50 96.9 0.057 19 10.2 14793
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 2.59 2.63 86.5 0.337 8.1 652
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 PDB entry 4HVC 2.59 35.54 13977 749 96.67 0.2291 0.2268 0.2236 0.272 0.2705 RANDOM 59.398
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] -1.33 -1.33 -1.33 4.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.34 r_dihedral_angle_3_deg 13.108 r_dihedral_angle_4_deg 10.846 r_dihedral_angle_1_deg 5.16 r_angle_refined_deg 1.045 r_angle_other_deg 0.695 r_chiral_restr 0.05 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.34 r_dihedral_angle_3_deg 13.108 r_dihedral_angle_4_deg 10.846 r_dihedral_angle_1_deg 5.16 r_angle_refined_deg 1.045 r_angle_other_deg 0.695 r_chiral_restr 0.05 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3741 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 30
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing