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Crystal structure of dihydropyrimidinase from Saccharomyces kluyveri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NFG PDB entry 1nfg
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 20% PEG 3350, 0.1M ammonium sulfate, 0.001mM zinc chloride, 0.1M bis-tris
, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.428 α = 90 b = 73.32 β = 91.59 c = 162.181 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 100 CCD ADSC QUANTUM 4 2004-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.931 ESRF ID14-2
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 2.4 44.3 99.3 0.086 13.5 3.1 83629 83629 44.9
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 2.4 2.53 98.7 0.309 3.2 3 12084
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 1nfg 2.4 43.85 79226 79226 4233 98.98 0.21996 0.21712 0.2218 0.2737 0.2162 RANDOM 35.905
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] -0.1 0.41 2.7 -2.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.512 r_dihedral_angle_4_deg 17.679 r_dihedral_angle_3_deg 15.726 r_dihedral_angle_1_deg 5.872 r_scangle_it 1.548 r_angle_refined_deg 1.193 r_scbond_it 0.983 r_mcangle_it 0.493 r_nbtor_refined 0.3 r_mcbond_it 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.512 r_dihedral_angle_4_deg 17.679 r_dihedral_angle_3_deg 15.726 r_dihedral_angle_1_deg 5.872 r_scangle_it 1.548 r_angle_refined_deg 1.193 r_scbond_it 0.983 r_mcangle_it 0.493 r_nbtor_refined 0.3 r_mcbond_it 0.296 r_symmetry_hbond_refined 0.246 r_symmetry_vdw_refined 0.228 r_nbd_refined 0.191 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16587 Nucleic Acid Atoms Solvent Atoms 681 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling EPMR phasing