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Pyrrolysine tRNA Synthetase bound to a pyrrolysine analogue (cyc) and ATP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 289 100 mM Tris
10% PEG2000 MME, pH 7.5, VAPOR DIFFUSION, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.39 63.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.773 α = 90 b = 104.773 β = 90 c = 71.594 γ = 120
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 315 2007-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.97917 NSLS X29A
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 1.9 40 99.6 0.078 29.3 10.8 35592 33104 1 1
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 1.9 1.97 96.5 0.328 5.2 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS THROUGHOUT 1.9 40 33104 1730 99.85 0.16374 0.16235 0.1662 0.18943 0.1956 RANDOM 35.272
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] -0.55 -0.27 -0.55 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.199 r_dihedral_angle_4_deg 13.094 r_dihedral_angle_3_deg 12.537 r_dihedral_angle_1_deg 6.047 r_scangle_it 5.814 r_scbond_it 4.453 r_mcangle_it 4.354 r_mcbond_it 3.946 r_angle_refined_deg 1.282 r_mcbond_other 0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.199 r_dihedral_angle_4_deg 13.094 r_dihedral_angle_3_deg 12.537 r_dihedral_angle_1_deg 6.047 r_scangle_it 5.814 r_scbond_it 4.453 r_mcangle_it 4.354 r_mcbond_it 3.946 r_angle_refined_deg 1.282 r_mcbond_other 0.92 r_angle_other_deg 0.812 r_symmetry_vdw_other 0.242 r_nbd_refined 0.206 r_nbd_other 0.195 r_symmetry_vdw_refined 0.18 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.162 r_symmetry_hbond_refined 0.148 r_nbtor_other 0.085 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2046 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling CCP4 phasing