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PROLYL-TRNA SYNTHETASE FROM ENTEROCOCCUS FAECALIS COMPLEXED WITH ATP, manganese and prolinol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J3L PDB ENTRY 2J3L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 20% PEG 6000, 1M LICL, 100MM MES, PH 6.5, 5MM PROLINOL, 2MM ATP, 6MM MGCL2
Crystal Properties Matthews coefficient Solvent content 2.4 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.583 α = 90 b = 92.679 β = 106.11 c = 101.223 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 100 CCD ADSC CCD 2004-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.3 30 99 0.1 6.44 3.7 54112
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 2.3 2.4 98.6 0.45 1.95 3.7
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 2J3L 2.3 29.49 52213 1894 100 0.198 0.196 0.1897 0.26 0.2507 RANDOM 21.84
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] -0.03 0.47 -0.26 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.853 r_dihedral_angle_4_deg 19.849 r_dihedral_angle_3_deg 16.968 r_dihedral_angle_1_deg 7.073 r_scangle_it 3.679 r_scbond_it 2.33 r_angle_refined_deg 1.694 r_mcangle_it 1.359 r_mcbond_it 0.828 r_symmetry_hbond_refined 0.341
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.853 r_dihedral_angle_4_deg 19.849 r_dihedral_angle_3_deg 16.968 r_dihedral_angle_1_deg 7.073 r_scangle_it 3.679 r_scbond_it 2.33 r_angle_refined_deg 1.694 r_mcangle_it 1.359 r_mcbond_it 0.828 r_symmetry_hbond_refined 0.341 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.241 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.19 r_chiral_restr 0.105 r_bond_refined_d 0.016 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_xyhbond_nbd_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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8791 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing