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Crystal Structure of human AlaRS catalytic domain with R329H mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HXU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 PEG3350
Crystal Properties Matthews coefficient Solvent content 2.3 46.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.848 α = 90 b = 121.172 β = 118.47 c = 68.012 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 173 PIXEL PSI PILATUS 6M 2011-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 1 SSRL BL11-1
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 1.38 50 98.3 29 3.6 185858
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 1.38 1.4 82.9 0.403 2.6 2.4 7807
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 3HXU 1.38 33.96 176334 9339 98.14 0.1841 0.1826 0.1802 0.2139 0.2108 RANDOM 20.396
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] -0.02 -0.26 0.25 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.565 r_sphericity_free 32.218 r_dihedral_angle_4_deg 14.097 r_dihedral_angle_3_deg 12.416 r_sphericity_bonded 10.324 r_dihedral_angle_1_deg 4.812 r_rigid_bond_restr 1.534 r_angle_refined_deg 1.118 r_chiral_restr 0.077 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.565 r_sphericity_free 32.218 r_dihedral_angle_4_deg 14.097 r_dihedral_angle_3_deg 12.416 r_sphericity_bonded 10.324 r_dihedral_angle_1_deg 4.812 r_rigid_bond_restr 1.534 r_angle_refined_deg 1.118 r_chiral_restr 0.077 r_bond_refined_d 0.006 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6008 Nucleic Acid Atoms Solvent Atoms 810 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-2000 data scaling MOLREP phasing