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Native crystal structure analysis on Arabidopsis dUTPase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q5H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 298 0.2 M ammonium sulfate, 0.1 M Tris-HCl pH 9.0, 0.02 M taurine, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.75 29.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.903 α = 90 b = 70.86 β = 90 c = 75.555 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 IMAGE PLATE RIGAKU RAXIS IV Blue 2006-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.542
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 2.2 50 99.3 0.075 57.1 5.4 19648 5
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 2.2 2.28 98.4 0.123 37.9 5.4
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 1Q5H 2.2 21.46 18428 992 99.29 0.18508 0.18151 0.1818 0.25075 0.2511 RANDOM 20.947
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.219 r_dihedral_angle_3_deg 18.013 r_dihedral_angle_4_deg 17.612 r_dihedral_angle_1_deg 8.048 r_scangle_it 4.901 r_scbond_it 3.141 r_angle_refined_deg 2.075 r_mcangle_it 1.843 r_mcbond_it 1.12 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.219 r_dihedral_angle_3_deg 18.013 r_dihedral_angle_4_deg 17.612 r_dihedral_angle_1_deg 8.048 r_scangle_it 4.901 r_scbond_it 3.141 r_angle_refined_deg 2.075 r_mcangle_it 1.843 r_mcbond_it 1.12 r_nbtor_refined 0.317 r_nbd_refined 0.229 r_symmetry_vdw_refined 0.228 r_symmetry_hbond_refined 0.187 r_chiral_restr 0.173 r_xyhbond_nbd_refined 0.133 r_bond_refined_d 0.023 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2865 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing