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Crystal structure of dihydropyrimidinase from Saccharomyces kluyveri in complex with the reaction product N-carbamyl-beta-alanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FTY PDB entry 2fty
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 20% PEG 3350, 0.1M trisodium citrate, 0.1M bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.19 43.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.141 α = 90 b = 73.027 β = 91.98 c = 164.105 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 IMAGE PLATE MARRESEARCH 2005-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.843 EMBL/DESY, HAMBURG BW7B
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 2.44 45 96.1 0.09 12.1 3.4 77328 77328 29.6
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 2.44 2.57 74 0.214 4.8 3 7593
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 2fty 2.45 44.37 73390 3922 97.26 0.18477 0.18199 0.1885 0.23743 0.2284 RANDOM 22.93
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 -0.3 1.07 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.516 r_dihedral_angle_4_deg 17.95 r_dihedral_angle_3_deg 15.033 r_dihedral_angle_1_deg 5.803 r_scangle_it 1.237 r_angle_refined_deg 1.177 r_scbond_it 0.795 r_mcangle_it 0.387 r_nbtor_refined 0.3 r_mcbond_it 0.231
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.516 r_dihedral_angle_4_deg 17.95 r_dihedral_angle_3_deg 15.033 r_dihedral_angle_1_deg 5.803 r_scangle_it 1.237 r_angle_refined_deg 1.177 r_scbond_it 0.795 r_mcangle_it 0.387 r_nbtor_refined 0.3 r_mcbond_it 0.231 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.187 r_symmetry_hbond_refined 0.166 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.08 r_metal_ion_refined 0.048 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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 16600 Nucleic Acid Atoms Solvent Atoms 795 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling