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Crystal structure of the complex of peptidyl tRNA hydrolase with a phosphate ion at the substrate binding site and cytarabine at a new ligand binding site at 1.1 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LWR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 HEPES, PEG 400, PEG 1500, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.02 38.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34 α = 90 b = 66.16 β = 90 c = 76.15 γ = 90
Symmetry Space Group P 21 21 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 MARRESEARCH Mirror 2013-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.1 16.85 96.9 13.3 3.8 68259
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.16
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 4LWR 1.1 16.85 64713 3454 96.65 0.12712 0.12543 0.1254 0.1593 0.1589 RANDOM 15.136
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] -0.16 -0.09 0.25
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 48.807 r_dihedral_angle_2_deg 34.348 r_sphericity_bonded 12.629 r_dihedral_angle_3_deg 11.871 r_rigid_bond_restr 10.748 r_dihedral_angle_4_deg 7.626 r_long_range_B_refined 5.996 r_dihedral_angle_1_deg 5.923 r_long_range_B_other 5.032 r_scangle_other 3.96
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 48.807 r_dihedral_angle_2_deg 34.348 r_sphericity_bonded 12.629 r_dihedral_angle_3_deg 11.871 r_rigid_bond_restr 10.748 r_dihedral_angle_4_deg 7.626 r_long_range_B_refined 5.996 r_dihedral_angle_1_deg 5.923 r_long_range_B_other 5.032 r_scangle_other 3.96 r_scbond_other 3.394 r_scbond_it 3.391 r_angle_other_deg 3.272 r_mcangle_other 2.999 r_mcangle_it 2.995 r_mcbond_other 2.589 r_mcbond_it 2.587 r_angle_refined_deg 2.166 r_chiral_restr 0.17 r_bond_refined_d 0.029 r_gen_planes_other 0.02 r_gen_planes_refined 0.013 r_bond_other_d 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1496 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing