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THE STRUCTURE OF LEISHMANIA PYRUVATE KINASE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PKY PDB ENTRY 1PKY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.8 6% PEG 4000, 20MM AMMONIUM SULPHATE, 15% GLYCEROL, 20MM SODIUM ACETATE PH 4.8
Crystal Properties Matthews coefficient Solvent content 3.33 62.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.649 α = 90 b = 132.638 β = 97.11 c = 180.996 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 BENT FUSED QUARTZ SINGLE SEGMENT MIRROR 1997-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX7.2 SRS PX7.2
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 2.35 30 68 0.089 5.4 1.5 160789
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 2.35 2.48 47.4 0.308 2.4 1.2
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION OTHER THROUGHOUT PDB ENTRY 1PKY 2.35 30 160789 8074 67.9 0.209 0.209 0.2239 0.256 RANDOM 48.9
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] -12.518 -4.1509 11.1994 1.3186
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 24 x_angle_deg 1.4 x_improper_angle_d 1.2 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
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 24 x_angle_deg 1.4 x_improper_angle_d 1.2 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 x_mcbond_it x_mcangle_it x_scbond_it x_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 29994 Nucleic Acid Atoms Solvent Atoms 2952 Heterogen Atoms 40
Software Software Software Name Purpose AMoRE phasing FFT model building SHELXS phasing MLPHARE phasing DM model building X-PLOR refinement DENZO data reduction CCP4 data scaling FFT phasing DM phasing