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Human Dihydropyrimidinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FTW PDB ENTRY 2FTW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1M HEPES PH 7.5, 70% MPD
Crystal Properties Matthews coefficient Solvent content 2.33 47.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.65 α = 90 b = 89.65 β = 90 c = 219.1 γ = 120
Symmetry Space Group P 64 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 CCD TOROIDAL ZERODUR MIRROR 2007-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.8 20 99 0.09 26.63 17.23 13425 2
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 2.8 2.9 99.1 0.66 6.01 17.94
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2FTW 2.8 19.95 12742 682 99.4 0.203 0.2 0.2022 0.251 0.2516 RANDOM 59.65
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] 4.45 2.23 4.45 -6.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.054 r_dihedral_angle_3_deg 15.41 r_dihedral_angle_4_deg 14.995 r_dihedral_angle_1_deg 4.911 r_angle_refined_deg 0.945 r_scangle_it 0.541 r_scbond_it 0.321 r_nbtor_refined 0.296 r_mcangle_it 0.273 r_nbd_refined 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.054 r_dihedral_angle_3_deg 15.41 r_dihedral_angle_4_deg 14.995 r_dihedral_angle_1_deg 4.911 r_angle_refined_deg 0.945 r_scangle_it 0.541 r_scbond_it 0.321 r_nbtor_refined 0.296 r_mcangle_it 0.273 r_nbd_refined 0.17 r_mcbond_it 0.152 r_symmetry_vdw_refined 0.144 r_xyhbond_nbd_refined 0.102 r_symmetry_hbond_refined 0.098 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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_refined 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3693 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing