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THE CRYSTAL STRUCTURE OF A COMPLEX OF CAMPYLOBACTER JEJUNI DUTPASE WITH SUBSTRATE ANALOGUE DUPNHPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W2Y PDB ENTRY 1W2Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 3.5 M SODIUM FORMATE PH 7.0, 20 MM MAGNESIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 2.9 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.397 α = 90 b = 93.397 β = 90 c = 143.634 γ = 90
Symmetry Space Group I 41 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 2004-07-21 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 1.7 30 97.8 0.05 37.1 8.1 33092 3
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 1.7 1.76 90.8 0.3 3.3 4.4
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1W2Y 1.7 30 31466 1700 94.2 0.162 0.159 0.176 0.206 RANDOM 20.21
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] 0.54 0.54 -1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.784 r_dihedral_angle_4_deg 16.907 r_dihedral_angle_3_deg 13.984 r_dihedral_angle_1_deg 5.544 r_scangle_it 3.786 r_scbond_it 2.74 r_angle_other_deg 1.967 r_angle_refined_deg 1.928 r_mcangle_it 1.842 r_mcbond_it 1.483
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.784 r_dihedral_angle_4_deg 16.907 r_dihedral_angle_3_deg 13.984 r_dihedral_angle_1_deg 5.544 r_scangle_it 3.786 r_scbond_it 2.74 r_angle_other_deg 1.967 r_angle_refined_deg 1.928 r_mcangle_it 1.842 r_mcbond_it 1.483 r_symmetry_hbond_refined 0.392 r_nbd_refined 0.349 r_xyhbond_nbd_refined 0.331 r_symmetry_vdw_other 0.285 r_symmetry_vdw_refined 0.281 r_nbd_other 0.26 r_chiral_restr 0.199 r_nbtor_refined 0.196 r_nbtor_other 0.095 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 1851 Nucleic Acid Atoms Solvent Atoms 478 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing