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Crystal structure of putative polyphosphate kinase 2 from Sinorhizobium meliloti
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 0.1 M Sodium formate, 0.1 M Lithium sulfate, 0.1 M Bis-tris buffer, 0.3 M NDSB-211, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.36 47.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.609 α = 75.86 b = 71.672 β = 85.97 c = 89.471 γ = 65.39
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 315 2007-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97920 APS 19-ID
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 2.23 34.7 89.4 0.066 15.2 3.6 56568 56568 59.8
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 2.23 2.31 46.8 0.381 1.99 2.2
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 (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 2.23 34.7 56551 56551 2840 89.28 0.18968 0.18696 0.1859 0.2403 0.238 RANDOM 57.022
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] -0.33 -0.19 0.04 0.74 0.52 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.533 r_dihedral_angle_4_deg 20.377 r_dihedral_angle_3_deg 18.879 r_dihedral_angle_1_deg 6.048 r_scangle_it 2.971 r_scbond_it 1.937 r_angle_refined_deg 1.431 r_mcangle_it 1.198 r_mcbond_it 0.746 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.533 r_dihedral_angle_4_deg 20.377 r_dihedral_angle_3_deg 18.879 r_dihedral_angle_1_deg 6.048 r_scangle_it 2.971 r_scbond_it 1.937 r_angle_refined_deg 1.431 r_mcangle_it 1.198 r_mcbond_it 0.746 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.301 r_nbd_refined 0.209 r_symmetry_hbond_refined 0.187 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.098 r_bond_refined_d 0.015 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 9418 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction PHENIX phasing