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Yeast inorganic pyrophosphatase 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
Crystal Properties Matthews coefficient Solvent content 2.57 52.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.915 α = 90 b = 93.549 β = 99.66 c = 69.168 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 2001-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM1A 0.8727 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 99.8 0.041 0.041 21.7 7.4 103964 103964
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 1.53 100 0.321 0.321 3.2 6946
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 19.92 103685 103685 5172 99.75 0.163 0.163 0.162 0.1618 0.18 0.1806 RANDOM 14.071
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 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.669 r_dihedral_angle_4_deg 13.811 r_dihedral_angle_3_deg 11.602 r_dihedral_angle_1_deg 6.465 r_scangle_it 2.94 r_scbond_it 2.121 r_angle_refined_deg 1.445 r_mcangle_it 1.295 r_mcbond_it 0.935 r_angle_other_deg 0.792
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.669 r_dihedral_angle_4_deg 13.811 r_dihedral_angle_3_deg 11.602 r_dihedral_angle_1_deg 6.465 r_scangle_it 2.94 r_scbond_it 2.121 r_angle_refined_deg 1.445 r_mcangle_it 1.295 r_mcbond_it 0.935 r_angle_other_deg 0.792 r_symmetry_vdw_other 0.229 r_nbd_refined 0.225 r_mcbond_other 0.191 r_nbd_other 0.18 r_nbtor_refined 0.177 r_chiral_restr 0.152 r_symmetry_hbond_refined 0.126 r_symmetry_vdw_refined 0.113 r_xyhbond_nbd_refined 0.111 r_nbtor_other 0.083 r_metal_ion_refined 0.063 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4447 Nucleic Acid Atoms Solvent Atoms 670 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction CCP4 data scaling MOLREP phasing