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Rhodopseudomonas palustris prolyl-tRNA synthetase in complex with ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other native R. palustris Prolyl-tRNA synthetase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1 M hepes (pH 7.0), 8-10 % PEG 8K, 5-10 % ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.89 57.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.2 α = 90 b = 211.21 β = 90 c = 148.21 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 2005-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.4 20 93.6 0.0086 4 70163 65656 2.4 2.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.55 93.7 0.474 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 native R. palustris Prolyl-tRNA synthetase 2.4 70163 63935 3397 95.97 0.20051 0.19735 0.1924 0.26104 0.2548 RANDOM 36.851
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] 1.48 -2.3 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.209 r_dihedral_angle_4_deg 19.099 r_dihedral_angle_3_deg 17.307 r_dihedral_angle_1_deg 6.524 r_scangle_it 2.72 r_scbond_it 1.761 r_angle_refined_deg 1.566 r_mcangle_it 1.227 r_mcbond_it 0.711 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.209 r_dihedral_angle_4_deg 19.099 r_dihedral_angle_3_deg 17.307 r_dihedral_angle_1_deg 6.524 r_scangle_it 2.72 r_scbond_it 1.761 r_angle_refined_deg 1.566 r_mcangle_it 1.227 r_mcbond_it 0.711 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.214 r_nbd_refined 0.212 r_symmetry_hbond_refined 0.205 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.098 r_metal_ion_refined 0.039 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10485 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction XSCALE data scaling MOLREP phasing