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Crystal structure of Human tRNase Z, short form (ELAC1).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other MODEL DETERMINED FROM SIRAS EXPERIMENT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 15% PEG 3350 0.2M NA NITRATE, pH 7
Crystal Properties Matthews coefficient Solvent content 2 38.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.52 α = 90 b = 73.79 β = 98.69 c = 73.66 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 QUANTUM 315 MIRRORS 2011-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.7 49.57 97 0.04 8.8 3.4 67111 2 7.82
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 1.7 1.79 95.3 0.04 2 3.2
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 MODEL DETERMINED FROM SIRAS EXPERIMENT 1.7 72.81 63620 3400 96.66 0.18776 0.18656 0.1888 0.21015 0.2119 RANDOM 27.713
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] 0.32 0.9 -0.24 0.19
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.212 r_sphericity_bonded 42.796 r_dihedral_angle_2_deg 35.555 r_dihedral_angle_4_deg 24.702 r_dihedral_angle_3_deg 11.776 r_dihedral_angle_1_deg 5.705 r_angle_refined_deg 1.49 r_angle_other_deg 1.27 r_chiral_restr 0.093 r_bond_refined_d 0.015
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.212 r_sphericity_bonded 42.796 r_dihedral_angle_2_deg 35.555 r_dihedral_angle_4_deg 24.702 r_dihedral_angle_3_deg 11.776 r_dihedral_angle_1_deg 5.705 r_angle_refined_deg 1.49 r_angle_other_deg 1.27 r_chiral_restr 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.004 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3903 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing