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Yeast inorganic pyrophosphatase variant D120E 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 51.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.654 α = 90 b = 93.191 β = 99.62 c = 69.379 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 2001-03-15 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 99.9 0.059 0.059 9.5 4.1 59922
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 99.9 0.388 0.388 1.9
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 19.61 56810 3024 100 0.16841 0.16659 0.1814 0.2028 0.2135 RANDOM 22.442
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_1_deg 6.787 r_scangle_it 3.644 r_scbond_it 2.285 r_angle_refined_deg 1.47 r_mcangle_it 1.458 r_angle_other_deg 0.853 r_mcbond_it 0.832 r_symmetry_vdw_other 0.305 r_nbd_other 0.243 r_nbd_refined 0.215
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.787 r_scangle_it 3.644 r_scbond_it 2.285 r_angle_refined_deg 1.47 r_mcangle_it 1.458 r_angle_other_deg 0.853 r_mcbond_it 0.832 r_symmetry_vdw_other 0.305 r_nbd_other 0.243 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.166 r_symmetry_hbond_refined 0.166 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.098 r_metal_ion_refined 0.088 r_nbtor_other 0.084 r_bond_refined_d 0.015 r_gen_planes_other 0.014 r_gen_planes_refined 0.01 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 4357 Nucleic Acid Atoms Solvent Atoms 528 Heterogen Atoms 15
Software Software Software Name Purpose MOLREP phasing REFMAC refinement DENZO data reduction CCP4 data scaling