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Crystal Structure of Polyphosphate Kinase from Porphyromonas Gingivalis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 2.6M MALIC ACID, PH 7.0, 0.5M AMMONIUM SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.91 57.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.33 α = 90 b = 99.33 β = 90 c = 335.061 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 MAR CCD 165 mm MIRRORS 2006-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.7 50 97.6 0.089 0.09 6 4.5 51199 51199 62.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.7 2.8 94.1 0.36 0.48 1.8 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.7 20 49169 49169 1578 99.43 0.19004 0.19004 0.1879 0.1881 0.25457 0.2558 RANDOM 72.398
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] 0.82 0.41 0.82 -1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.003 r_dihedral_angle_3_deg 19.929 r_dihedral_angle_4_deg 17.639 r_scangle_it 16.841 r_scbond_it 13.353 r_mcangle_it 10.771 r_mcbond_it 8.305 r_dihedral_angle_1_deg 7.144 r_angle_refined_deg 1.301 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.003 r_dihedral_angle_3_deg 19.929 r_dihedral_angle_4_deg 17.639 r_scangle_it 16.841 r_scbond_it 13.353 r_mcangle_it 10.771 r_mcbond_it 8.305 r_dihedral_angle_1_deg 7.144 r_angle_refined_deg 1.301 r_nbtor_refined 0.322 r_symmetry_hbond_refined 0.189 r_nbd_refined 0.187 r_symmetry_vdw_refined 0.174 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.088 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 10331 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 65
Software Software Software Name Purpose SHELX model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SHELX phasing