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Crystal Structure of Human Dihydropyrimidinease-like 2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 18% PEG 10k, 0.1M Tris, 0.2M CaCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.34 47.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.4 α = 90 b = 126.1 β = 113 c = 102.9 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 173 CCD ADSC QUANTUM 4 MIRRORS 2006-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 2.4 30 99.7 0.143 9.6 4.3 79391 79142 1 1 27.7
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) 2.4 2.6 99.7 0.43 3.36 4.3 16757
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.4 29.31 2 79190 75230 3960 99.96 0.173 0.169 0.174 0.245 0.2458 RANDOM 18.36
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] 0.02 -0.02 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.662 r_dihedral_angle_4_deg 18.892 r_dihedral_angle_3_deg 16.135 r_dihedral_angle_1_deg 6.572 r_scangle_it 2.586 r_scbond_it 1.697 r_angle_refined_deg 1.567 r_mcangle_it 1.153 r_angle_other_deg 0.98 r_mcbond_it 0.696
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.662 r_dihedral_angle_4_deg 18.892 r_dihedral_angle_3_deg 16.135 r_dihedral_angle_1_deg 6.572 r_scangle_it 2.586 r_scbond_it 1.697 r_angle_refined_deg 1.567 r_mcangle_it 1.153 r_angle_other_deg 0.98 r_mcbond_it 0.696 r_symmetry_vdw_other 0.217 r_nbd_refined 0.207 r_nbd_other 0.198 r_xyhbond_nbd_refined 0.195 r_nbtor_refined 0.176 r_symmetry_vdw_refined 0.171 r_metal_ion_refined 0.167 r_symmetry_hbond_refined 0.139 r_mcbond_other 0.128 r_chiral_restr 0.089 r_nbtor_other 0.088 r_bond_refined_d 0.015 r_xyhbond_nbd_other 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14638 Nucleic Acid Atoms Solvent Atoms 849 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement ProDC data collection XDS data scaling MOLREP phasing