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Crystal structure of dihydropyrimidinase from dictyostelium discoideum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KCX PDB ENTRY 1KCX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 25% PEG 1500, 0.1M MMT buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 43.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.6 α = 90 b = 89.599 β = 90 c = 134.953 γ = 90
Symmetry Space Group I 2 2 2
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 2005-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.939 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 45.459 94.4 0.134 0.134 4.3 3.1 30568 25.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.16 94.4 94.3 0.662 0.662 0.9 2.8 30568
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 (All) 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 1KCX 2.05 25 30551 30551 1557 93.91 0.207 0.204 0.204 0.2121 0.252 0.2574 RANDOM 23.157
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] -2.63 1.37 1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.413 r_dihedral_angle_4_deg 17.318 r_dihedral_angle_3_deg 13.704 r_dihedral_angle_1_deg 5.884 r_scangle_it 1.745 r_angle_refined_deg 1.182 r_scbond_it 1.166 r_angle_other_deg 0.79 r_mcangle_it 0.708 r_mcbond_it 0.608
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.413 r_dihedral_angle_4_deg 17.318 r_dihedral_angle_3_deg 13.704 r_dihedral_angle_1_deg 5.884 r_scangle_it 1.745 r_angle_refined_deg 1.182 r_scbond_it 1.166 r_angle_other_deg 0.79 r_mcangle_it 0.708 r_mcbond_it 0.608 r_symmetry_vdw_other 0.203 r_nbd_refined 0.196 r_nbd_other 0.186 r_nbtor_refined 0.171 r_symmetry_hbond_refined 0.157 r_xyhbond_nbd_refined 0.155 r_mcbond_other 0.099 r_symmetry_vdw_refined 0.085 r_nbtor_other 0.084 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_metal_ion_refined 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3748 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 9
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling