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Pyridoxal Kinase from Leishmania donovani in complex with ADP and Pyridoxine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 17% PEG 8000, 0.1M Sodium Cacodylate, 0.32M Calcium Acetate, 6% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.11 41.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.7 α = 90 b = 71.69 β = 99.28 c = 77.14 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 MAR scanner 345 mm plate 2018-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 43.12 95 10.1 2.9 37788
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.04 91.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2 43.12 35946 1852 94.71 0.1758 0.17366 0.1822 0.21785 0.2225 RANDOM 17.329
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] 0.12 -0.15 0.22 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.456 r_dihedral_angle_4_deg 18.36 r_dihedral_angle_3_deg 13.011 r_dihedral_angle_1_deg 7.045 r_long_range_B_refined 4.155 r_long_range_B_other 4.051 r_scangle_other 2.681 r_mcangle_it 2.375 r_mcangle_other 2.375 r_scbond_it 1.759
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.456 r_dihedral_angle_4_deg 18.36 r_dihedral_angle_3_deg 13.011 r_dihedral_angle_1_deg 7.045 r_long_range_B_refined 4.155 r_long_range_B_other 4.051 r_scangle_other 2.681 r_mcangle_it 2.375 r_mcangle_other 2.375 r_scbond_it 1.759 r_scbond_other 1.728 r_angle_refined_deg 1.553 r_mcbond_it 1.484 r_mcbond_other 1.484 r_angle_other_deg 1.406 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4349 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing