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Crystal structure of dihydropyrimidinase from Pseudomonas aeruginosa PAO1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FTW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.5 298 10% PEG8000, 100mM HEPES sodium salt, 200mM Calcium Acetate
Crystal Properties Matthews coefficient Solvent content 2.75 55.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.134 α = 90 b = 112.134 β = 90 c = 161.05 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD RAYONIX MX300HE 2015-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 0.975 NSRRC BL13C1
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 2.1 97.11 99.9 0.085 19.21 6 68937 68799
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 2.1 2.18 99.9 0.59 2.976 5.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2FTW 2.1 97.11 65158 3471 99.56 0.17191 0.16957 0.21546 0.2096 RANDOM 29.554
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] -0.03 -0.02 -0.03 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.995 r_dihedral_angle_4_deg 18.921 r_dihedral_angle_3_deg 14.662 r_dihedral_angle_1_deg 6.43 r_long_range_B_refined 6.344 r_long_range_B_other 6.325 r_scangle_other 5.103 r_scbond_it 3.409 r_scbond_other 3.408 r_mcangle_it 3.383
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.995 r_dihedral_angle_4_deg 18.921 r_dihedral_angle_3_deg 14.662 r_dihedral_angle_1_deg 6.43 r_long_range_B_refined 6.344 r_long_range_B_other 6.325 r_scangle_other 5.103 r_scbond_it 3.409 r_scbond_other 3.408 r_mcangle_it 3.383 r_mcangle_other 3.383 r_mcbond_it 2.446 r_mcbond_other 2.442 r_angle_refined_deg 1.879 r_angle_other_deg 0.9 r_chiral_restr 0.117 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7356 Nucleic Acid Atoms Solvent Atoms 338 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction MOLREP phasing