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DUTPase from phage phi11 of S.aureus: visualization of the species-specific insert
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PY4 PDB ENTRY 2PY4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 25% MPD, 0.02M calcium chloride, 0.1M sodium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.31 46.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.66 α = 90 b = 109.66 β = 90 c = 169.27 γ = 90
Symmetry Space Group P 43 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 PIXEL DECTRIS PILATUS 2M-F MIRRORS 2012-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 47.104 60917 -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 2.1 2.15 0.978 3.07 12.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2PY4 2.1 47.1 57719 3140 99.96 0.1858 0.18303 0.23224 0.2208 RANDOM 50.655
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] 0.26 0.26 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.156 r_dihedral_angle_4_deg 21.962 r_dihedral_angle_3_deg 13.586 r_dihedral_angle_1_deg 7.972 r_scangle_it 3.765 r_scbond_it 2.618 r_angle_refined_deg 1.888 r_mcangle_it 1.677 r_mcbond_it 1.036 r_angle_other_deg 1.024
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.156 r_dihedral_angle_4_deg 21.962 r_dihedral_angle_3_deg 13.586 r_dihedral_angle_1_deg 7.972 r_scangle_it 3.765 r_scbond_it 2.618 r_angle_refined_deg 1.888 r_mcangle_it 1.677 r_mcbond_it 1.036 r_angle_other_deg 1.024 r_mcbond_other 0.363 r_chiral_restr 0.103 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_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 6786 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 176
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling