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REFINED STRUCTURE OF YEAST INORGANIC PYROPHOSPHATASE AND ITS K61R MUTANT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PYP LOW RESOLUTION STRUCTURE (PDB ENTRY 1PYP)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microliter drops 6.5 277 CRYSTALLIZATION CONDITIONS: 10 MG/ML PROTEIN IN 0.1 M MES (PH 6.5) BUFFER. 10 MICROLITER DROPS IN 9 WELL DEPRESSION PLATE IN A PLASTIC SANDWICH BOX CONTAINING 15 MILLILITER OF 0.1 M MES(PH 6.5) + 16 % MPD. EVERY ALTERNATE DAY, MPD CONCENTRATION INCREASED BY 1 % UNTIL FINAL CONCENTRATION REACHED 25 %. 4 DEGREE C. WITHIN 15 DAYS, 0.2 X 0.3 X 0.4 MM CRYSTALS., microliter drops, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.6 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.09 α = 90 b = 93.06 β = 99.62 c = 51.58 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 93 IMAGE PLATE RIGAKU RAXIS MSC/YALE MIRRORS 1995-03-25 M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1
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 2.23 30 91.7 0.044 2.7 28288 14.1
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 LOW RESOLUTION STRUCTURE (PDB ENTRY 1PYP) 2.2 8 27238 2704 85.1 0.193 0.193 0.1839 0.288 0.2707 RANDOM 15.5
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 x_dihedral_angle_d 26.5 x_scangle_it 5.1 x_scbond_it 3.62 x_mcangle_it 3.14 x_mcbond_it 2.18 x_improper_angle_d 2 x_angle_deg 1.1 x_bond_d 0.009 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 26.5 x_scangle_it 5.1 x_scbond_it 3.62 x_mcangle_it 3.14 x_mcbond_it 2.18 x_improper_angle_d 2 x_angle_deg 1.1 x_bond_d 0.009 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4492 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 2
Software Software Software Name Purpose X-PLOR model building X-PLOR refinement DENZO data reduction X-PLOR phasing