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Structure of glutamyl-tRNA synthetase (Xoo1504) from Xanthomonas oryzae pv. oryzae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CFO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 287 55%(v/v) Tacsimate, 0.1M bistris propane pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.54 51.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.353 α = 90 b = 107.937 β = 96.24 c = 165.895 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 293 CCD ADSC QUANTUM 270 2008-05-04 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.96 Photon Factory BL-17A
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 3 50 90.6 0.087 10.4 2.1 59553
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 3 3.11 65.7 0.31 1.8 1.8
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 2CFO 3 29.44 56448 3046 90.2 0.204 0.2 0.2059 0.291 0.2889 RANDOM 70.66
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] -0.79 1.07 -3.44 3.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.537 r_dihedral_angle_3_deg 21.612 r_dihedral_angle_4_deg 19.714 r_long_range_B_refined 9.023 r_long_range_B_other 9.022 r_dihedral_angle_1_deg 7.803 r_mcangle_it 6.045 r_mcangle_other 6.045 r_scangle_other 5.372 r_mcbond_it 3.676
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.537 r_dihedral_angle_3_deg 21.612 r_dihedral_angle_4_deg 19.714 r_long_range_B_refined 9.023 r_long_range_B_other 9.022 r_dihedral_angle_1_deg 7.803 r_mcangle_it 6.045 r_mcangle_other 6.045 r_scangle_other 5.372 r_mcbond_it 3.676 r_mcbond_other 3.676 r_scbond_it 3.171 r_scbond_other 3.171 r_angle_refined_deg 1.598 r_angle_other_deg 1.085 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 21616 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing