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Saccharomyces cerevisiae cytosolic exopolyphosphatase, phosphate complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QB6 PDB entry 2QB6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 291 7% PEG 4000, 150 mM (NH4)2SO4, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.19 43.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.992 α = 90 b = 83.039 β = 90 c = 118.9 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 CCD ADSC QUANTUM 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.93400 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 68 94.6 0.054 5.8 3.7 99085
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.69 74.9 0.266 2.8 2.2 11292
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2QB6 1.6 67.42 94073 4945 94.4 0.17216 0.17062 0.20139 RANDOM 24.4
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] -0.56 1.09 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.493 r_dihedral_angle_4_deg 13.579 r_dihedral_angle_3_deg 13.533 r_dihedral_angle_1_deg 5.538 r_scangle_it 2.628 r_scbond_it 1.829 r_angle_refined_deg 1.433 r_angle_other_deg 1.253 r_mcangle_it 1.039 r_mcbond_it 0.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.493 r_dihedral_angle_4_deg 13.579 r_dihedral_angle_3_deg 13.533 r_dihedral_angle_1_deg 5.538 r_scangle_it 2.628 r_scbond_it 1.829 r_angle_refined_deg 1.433 r_angle_other_deg 1.253 r_mcangle_it 1.039 r_mcbond_it 0.939 r_symmetry_vdw_other 0.263 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.196 r_nbtor_refined 0.176 r_nbd_other 0.174 r_symmetry_hbond_refined 0.153 r_mcbond_other 0.151 r_xyhbond_nbd_refined 0.13 r_nbtor_other 0.084 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6287 Nucleic Acid Atoms Solvent Atoms 784 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling REFMAC phasing