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Crystal structure of dihydropyrimidinase from Brevibacillus agri NCHU1002
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K1D PDB ENTRY 1K1D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 293 0.1M Na-Acetate, 32% MPD, 0.04M CaCl2, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.5 50.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.807 α = 90 b = 109.112 β = 90 c = 140.984 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 IMAGE PLATE MAR scanner 345 mm plate 2004-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL17B2 1.0 NSRRC BL17B2
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 1.73 30 99.6 100854 100472 5 5
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 1.73 1.79 92.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 PDB ENTRY 1K1D 1.73 30 100235 95236 4999 94.16 0.14874 0.14657 0.1469 0.18958 0.1885 RANDOM 20.455
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] -0.25 0.73 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.692 r_dihedral_angle_4_deg 16.261 r_dihedral_angle_3_deg 13.507 r_dihedral_angle_1_deg 7.189 r_scangle_it 4.422 r_scbond_it 2.937 r_mcangle_it 2.922 r_mcbond_it 2 r_angle_refined_deg 1.412 r_chiral_restr 0.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.692 r_dihedral_angle_4_deg 16.261 r_dihedral_angle_3_deg 13.507 r_dihedral_angle_1_deg 7.189 r_scangle_it 4.422 r_scbond_it 2.937 r_mcangle_it 2.922 r_mcbond_it 2 r_angle_refined_deg 1.412 r_chiral_restr 0.134 r_bond_refined_d 0.018 r_gen_planes_refined 0.015 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7108 Nucleic Acid Atoms Solvent Atoms 1140 Heterogen Atoms 28
Software Software Software Name Purpose SPEC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling