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Pyruvate Phosphate Dikinase with bound Mg-PEP from Maize
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VBG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 PEG8000, magnesium sulfate, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.2 61.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.339 α = 90 b = 100.51 β = 98.48 c = 108.155 γ = 90
Symmetry Space Group C 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 RIGAKU RAXIS V 2000-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45PX 1.02 SPring-8 BL45PX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.3 45.63 99.9 0.075 7.5 4.04 51442 51391 1 1 31
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 2.3 2.44 99 0.255 2.5
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 (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 1VBG 2.3 45.63 51511 50481 2528 98 0.238 0.23 0.2311 0.259 0.2605 RANDOM 52.6
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] 4.87 8.62 -5.75 0.88
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.1 c_scangle_it 2.98 c_mcangle_it 2.05 c_scbond_it 2.01 c_mcbond_it 1.26 c_angle_deg 1.2 c_improper_angle_d 0.84 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.1 c_scangle_it 2.98 c_mcangle_it 2.05 c_scbond_it 2.01 c_mcbond_it 1.26 c_angle_deg 1.2 c_improper_angle_d 0.84 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6385 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 16
Software Software Software Name Purpose CNS refinement CrystalClear data scaling CNS phasing