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Crystal structure of apo dUT1p from Saccharomyces cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F4F PDB entry 3F4F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 295 0.1M Ammonium sulfate, 0.1M Bis-Tris pH 5.5, 25% PEG 3350 plus 0.015 mg/mL Trypsin. Cryoprotected with a solution of 7% Glycerol, 7% Ethylene glycol and 7% Sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.97 37.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.461 α = 98.79 b = 95.466 β = 97.42 c = 97.594 γ = 107.13
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 RIGAKU RAXIS IV++ mirrors 2008-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
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 50 89.2 0.058 19.13 3.4 214470 191238 30.8
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 2.07 88.3 0.441 3.45 3.2 19074
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 3F4F 2 40.62 191230 9588 88.66 0.17783 0.17475 0.1734 0.23581 0.2336 RANDOM 22.395
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.004 r_dihedral_angle_4_deg 21.256 r_dihedral_angle_3_deg 16.177 r_dihedral_angle_1_deg 7.777 r_scangle_it 4.094 r_scbond_it 2.642 r_angle_refined_deg 1.851 r_mcangle_it 1.4 r_mcbond_it 0.884 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.004 r_dihedral_angle_4_deg 21.256 r_dihedral_angle_3_deg 16.177 r_dihedral_angle_1_deg 7.777 r_scangle_it 4.094 r_scbond_it 2.642 r_angle_refined_deg 1.851 r_mcangle_it 1.4 r_mcbond_it 0.884 r_nbtor_refined 0.309 r_nbd_refined 0.222 r_symmetry_hbond_refined 0.216 r_symmetry_vdw_refined 0.215 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.119 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22599 Nucleic Acid Atoms Solvent Atoms 1732 Heterogen Atoms 397
Software Software Software Name Purpose CrystalClear data collection PHASER phasing MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling