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Yeast inorganic pyrophosphatase variant D152E with magnesium and phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HUK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 277 16% MPD, 10 MM MGCL2, 1 MM PO4-, PH 6.0, VAPOR DIFFUSION, TEMPERATURE 277K, pH 6.00
Crystal Properties Matthews coefficient Solvent content 2.58 52.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.771 α = 90 b = 93.224 β = 100.01 c = 70.113 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 2001-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM1A 0.8000 ESRF BM1A
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 1.5 100 97.7 0.035 0.035 33.2 8.3 102428
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) 1.5 1.55 88.6 0.154 0.154 6.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1HUK 1.5 19.87 97201 5150 97.9 0.16034 0.15916 0.1597 0.18256 0.1829 RANDOM 13.869
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.268 r_dihedral_angle_4_deg 14.929 r_dihedral_angle_3_deg 11.868 r_dihedral_angle_1_deg 6.381 r_scangle_it 2.719 r_scbond_it 1.956 r_angle_refined_deg 1.301 r_mcangle_it 1.236 r_mcbond_it 0.872 r_angle_other_deg 0.776
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.268 r_dihedral_angle_4_deg 14.929 r_dihedral_angle_3_deg 11.868 r_dihedral_angle_1_deg 6.381 r_scangle_it 2.719 r_scbond_it 1.956 r_angle_refined_deg 1.301 r_mcangle_it 1.236 r_mcbond_it 0.872 r_angle_other_deg 0.776 r_symmetry_vdw_other 0.29 r_nbd_refined 0.226 r_symmetry_vdw_refined 0.214 r_symmetry_hbond_refined 0.2 r_nbtor_refined 0.18 r_nbd_other 0.179 r_mcbond_other 0.169 r_xyhbond_nbd_refined 0.115 r_nbtor_other 0.082 r_chiral_restr 0.08 r_metal_ion_refined 0.055 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other 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 4488 Nucleic Acid Atoms Solvent Atoms 759 Heterogen Atoms 18
Software Software Software Name Purpose MOLREP phasing REFMAC refinement DENZO data reduction CCP4 data scaling