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PYRUVATE PHOSPHATE DIKINASE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KC7 PPDK + phosphonopyruvate (PDB entry 1KC7)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 303 50-54% saturated ammonium sulfate, 10 mg/ml protein solution in 100mM KCl and 20mM imidazole buffer (pH 6.5), 100 mM Hepes buffer (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.81 56.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.837 α = 90 b = 58.838 β = 94.839 c = 102.949 γ = 90
Symmetry Space Group P 1 2 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 1995-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 1.3 NSLS X12C
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 1.9 20 93.5 0.051 0.051 23.7 79262 79262
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 80.1 0.405 2.9 6736
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FOURIER SYNTHESIS THROUGHOUT PPDK + phosphonopyruvate (PDB entry 1KC7) 1.94 20 2.2 75531 72384 4390 90.9 0.2064 0.2008 0.195 0.1942 0.257 0.2555 RANDOM 37.9
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 o_angle_deg 1.91 o_bond_d 0.021 o_bond_d_na o_bond_d_prot o_angle_d o_angle_d_na o_angle_d_prot o_angle_deg_na o_angle_deg_prot o_dihedral_angle_d
RMS Deviations Key Refinement Restraint Deviation o_angle_deg 1.91 o_bond_d 0.021 o_bond_d_na o_bond_d_prot o_angle_d o_angle_d_na o_angle_d_prot o_angle_deg_na o_angle_deg_prot o_dihedral_angle_d o_dihedral_angle_d_na o_dihedral_angle_d_prot o_improper_angle_d o_improper_angle_d_na o_improper_angle_d_prot o_mcbond_it o_mcangle_it o_scbond_it o_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6752 Nucleic Acid Atoms Solvent Atoms 879 Heterogen Atoms 26
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement