☰ Navigation Tabs
Crystal structure of catalytic fragment of human AlaRS in complex with Aze-SA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XEM PDB entry 4XEM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 310 25% PEG6000, 100 mM Tris-HCl, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.04 39.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.33 α = 90 b = 67.27 β = 136.23 c = 86.35 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 MAR scanner 345 mm plate 2011-12-15 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 Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.03 59.734 99.2 0.06 0.069 0.034 15.7 3.9 27565
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.03 2.14 94.8 0.32 0.32 0.373 0.189 2.4 3.7 3800
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 4XEM 2.03 59.73 26163 1390 99.44 0.1817 0.1799 0.1897 0.2146 0.2225 RANDOM 26.974
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] -0.75 -1.12 0.62 -1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.807 r_dihedral_angle_4_deg 17.112 r_dihedral_angle_3_deg 12.345 r_dihedral_angle_1_deg 4.716 r_angle_refined_deg 1.227 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2996 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 29
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing