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Saccharomyces cerevisiae cytosolic exopolyphosphatase, ATP 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 Ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.18 43.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.134 α = 90 b = 82.847 β = 90 c = 121.761 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 ID14-2 0.93300 ESRF ID14-2
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 1.9 30.5 99.4 0.065 7.7 4 60043
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) 1.9 2 99.9 0.327 1.6 3.9 8715
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 1.9 30.5 59362 3122 99.25 0.18633 0.18389 0.23287 RANDOM 26
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] 0.36 -0.41 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.63 r_scangle_it 2.878 r_metal_ion_refined 1.954 r_scbond_it 1.683 r_mcangle_it 1.236 r_angle_refined_deg 1.15 r_angle_other_deg 1.137 r_mcbond_it 0.663 r_symmetry_vdw_other 0.25 r_symmetry_hbond_refined 0.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.63 r_scangle_it 2.878 r_metal_ion_refined 1.954 r_scbond_it 1.683 r_mcangle_it 1.236 r_angle_refined_deg 1.15 r_angle_other_deg 1.137 r_mcbond_it 0.663 r_symmetry_vdw_other 0.25 r_symmetry_hbond_refined 0.229 r_nbd_other 0.227 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.181 r_xyhbond_nbd_refined 0.172 r_nbtor_other 0.081 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_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 6286 Nucleic Acid Atoms Solvent Atoms 643 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling REFMAC phasing