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The crystal structure of a complex of Campylobacter jejuni dUTPase with substrate analogue dUpNHp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OGK PDB ENTRY 1OGK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 25-30% MPD, 5% ISOPROPANOL, 50 MM MG-ACETATE, 100 MM HEPES PH 7.0
Crystal Properties Matthews coefficient Solvent content 2 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.963 α = 90 b = 70.629 β = 90 c = 92.85 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 100 2003-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 1.65 50 99.4 0.06 34 5.2 53061 2.7
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 1.65 1.71 98.5 0.45 2.7
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1OGK 1.65 55.9 50185 2693 99 0.153 0.151 0.2371 0.194 RANDOM 29.23
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] 0.4 -0.23 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.643 r_dihedral_angle_4_deg 25.195 r_dihedral_angle_3_deg 13.27 r_scangle_it 5.414 r_dihedral_angle_1_deg 4.872 r_scbond_it 4.327 r_mcangle_it 2.599 r_mcbond_it 2.134 r_angle_refined_deg 1.581 r_angle_other_deg 1.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.643 r_dihedral_angle_4_deg 25.195 r_dihedral_angle_3_deg 13.27 r_scangle_it 5.414 r_dihedral_angle_1_deg 4.872 r_scbond_it 4.327 r_mcangle_it 2.599 r_mcbond_it 2.134 r_angle_refined_deg 1.581 r_angle_other_deg 1.222 r_symmetry_vdw_other 0.254 r_nbd_refined 0.248 r_symmetry_vdw_refined 0.232 r_symmetry_hbond_refined 0.222 r_xyhbond_nbd_refined 0.195 r_nbtor_refined 0.194 r_nbd_other 0.178 r_chiral_restr 0.104 r_nbtor_other 0.089 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_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 3599 Nucleic Acid Atoms Solvent Atoms 383 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling MOLREP phasing