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Yeast inorganic pyrophosphatase variant D117E 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 2.55 51.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.763 α = 90 b = 93.23 β = 99.58 c = 69.215 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 RIGAKU MULTILAYER 2001-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.8 100 99.3 0.056 0.056 9.8 3.5 59558
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) 1.8 1.85 98.1 0.323 0.323 2.4
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 1.8 19.88 56482 3002 100 0.16297 0.16152 0.1736 0.18963 0.1963 RANDOM 22.889
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.54 r_scangle_it 3.66 r_scbond_it 2.263 r_mcangle_it 1.443 r_angle_refined_deg 1.41 r_angle_other_deg 0.82 r_mcbond_it 0.805 r_symmetry_vdw_other 0.334 r_nbd_other 0.245 r_nbd_refined 0.219
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.54 r_scangle_it 3.66 r_scbond_it 2.263 r_mcangle_it 1.443 r_angle_refined_deg 1.41 r_angle_other_deg 0.82 r_mcbond_it 0.805 r_symmetry_vdw_other 0.334 r_nbd_other 0.245 r_nbd_refined 0.219 r_symmetry_hbond_refined 0.135 r_xyhbond_nbd_refined 0.114 r_chiral_restr 0.09 r_nbtor_other 0.083 r_metal_ion_refined 0.059 r_symmetry_vdw_refined 0.022 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 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 4421 Nucleic Acid Atoms Solvent Atoms 437 Heterogen Atoms 10
Software Software Software Name Purpose MOLREP phasing REFMAC refinement DENZO data reduction CCP4 data scaling