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Rhodopseudomonas palustris prolyl-tRNA synthetase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.1 M citric acid (pH 5.5), 15-17 % PEG 3000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.87 57.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.84 α = 90 b = 212.56 β = 90 c = 150.56 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 2004-02-28 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 210 2004-02-01 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1 2 SYNCHROTRON ESRF BEAMLINE ID29 0.97917, 0.97927 ESRF ID29
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 1.96 20 91.3 0.0075 5 127056 116008 1.96 1.96
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 1.96 2.03 56.5 0.511
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD followed by molecular replacement THROUGHOUT 2 120017 109746 5809 96.6 0.19241 0.19091 0.1877 0.22124 RANDOM 29.878
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] 1.08 -0.7 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.437 r_dihedral_angle_4_deg 17.491 r_dihedral_angle_3_deg 14.434 r_dihedral_angle_1_deg 6.036 r_scangle_it 3.626 r_scbond_it 2.351 r_angle_refined_deg 1.416 r_mcangle_it 1.408 r_mcbond_it 0.948 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.437 r_dihedral_angle_4_deg 17.491 r_dihedral_angle_3_deg 14.434 r_dihedral_angle_1_deg 6.036 r_scangle_it 3.626 r_scbond_it 2.351 r_angle_refined_deg 1.416 r_mcangle_it 1.408 r_mcbond_it 0.948 r_nbtor_refined 0.301 r_symmetry_hbond_refined 0.228 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.129 r_xyhbond_nbd_other 0.122 r_chiral_restr 0.099 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_metal_ion_refined 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 10469 Nucleic Acid Atoms Solvent Atoms 623 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection XDS data reduction XSCALE data scaling SHELXD phasing SHARP phasing SOLVE phasing