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Crystal structure of deoxyuridine 5-triphosphate nucleotidohydrolase from Brucella melitensis, rhombohedral crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MBQ pdb entry 3MBQ, orthorhombic crystal form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 290 MD PACT SCREEN, E12: 20% PEG 3350, 200MM NA MALONATE, BRABA.10050.A AT 9.7MG/ML, pH 7.40, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.24 45.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.88 α = 90 b = 67.88 β = 90 c = 95.89 γ = 120
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 315r 2010-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 SSRL BL7-1
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 1.45 50.12 99.8 0.029 30.1 4.6 29210 29143 -3 23.78
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) 1.45 1.49 100 0.467 3.2 4.6 2204
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 3MBQ, orthorhombic crystal form 1.45 50 29210 29143 1475 99.8 0.151 0.151 0.15 0.1584 0.167 0.173 RANDOM 14.88
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] -0.05 -0.02 -0.05 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.934 r_dihedral_angle_4_deg 14.104 r_dihedral_angle_3_deg 10.053 r_dihedral_angle_1_deg 7.378 r_scangle_it 4.233 r_scbond_it 2.664 r_mcangle_it 1.856 r_angle_refined_deg 1.683 r_mcbond_it 1.091 r_angle_other_deg 0.978
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.934 r_dihedral_angle_4_deg 14.104 r_dihedral_angle_3_deg 10.053 r_dihedral_angle_1_deg 7.378 r_scangle_it 4.233 r_scbond_it 2.664 r_mcangle_it 1.856 r_angle_refined_deg 1.683 r_mcbond_it 1.091 r_angle_other_deg 0.978 r_mcbond_other 0.325 r_chiral_restr 0.106 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1036 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 4
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling