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Crystal structure of dihydropyrimidinase from Sinorhizobium meliloti
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YNY 1YNY, 1KCX, 1K1D experimental model PDB 1KCX 1YNY, 1KCX, 1K1D experimental model PDB 1K1D 1YNY, 1KCX, 1K1D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 4.6 293 4.0M sodium formate, 0.1M sodium acetate, pH 4.6, COUNTER-DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.61 65.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.887 α = 90 b = 126.281 β = 90 c = 196.104 γ = 90
Symmetry Space Group C 2 2 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 BRUKER SMART 6000 Montel mirrors 2006-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.85 39.89 98.4 0.0662 13 3.47 129593 14
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.9 89.1 0.311 3.11 1.83 8930
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 1YNY, 1KCX, 1K1D 1.85 29.6 129519 6524 98.46 0.149 0.148 0.1479 0.176 0.1754 RANDOM 5.383
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] 0.01 0.03 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.226 r_dihedral_angle_4_deg 17.585 r_dihedral_angle_3_deg 11.217 r_dihedral_angle_1_deg 10.5 r_scangle_it 2.835 r_scbond_it 2.021 r_angle_refined_deg 1.644 r_mcangle_it 1.168 r_mcbond_it 0.918 r_angle_other_deg 0.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.226 r_dihedral_angle_4_deg 17.585 r_dihedral_angle_3_deg 11.217 r_dihedral_angle_1_deg 10.5 r_scangle_it 2.835 r_scbond_it 2.021 r_angle_refined_deg 1.644 r_mcangle_it 1.168 r_mcbond_it 0.918 r_angle_other_deg 0.332 r_nbtor_refined 0.299 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.198 r_symmetry_vdw_refined 0.192 r_symmetry_hbond_refined 0.187 r_chiral_restr 0.146 r_nbd_other 0.135 r_metal_ion_refined 0.056 r_bond_refined_d 0.028 r_gen_planes_refined 0.009 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7313 Nucleic Acid Atoms Solvent Atoms 1338 Heterogen Atoms 36
Software Software Software Name Purpose SAINT data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction SAINT data reduction