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Pyridoxal kinase of Entamoeba histolytica with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Native Pyridoxal Kinase from Entamoeba histolytica
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 273 15% Peg4000, 100mM Tris pH7.5, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.14 42.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.256 α = 89.94 b = 44.272 β = 102.89 c = 75.246 γ = 107.03
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 2014-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.953 ESRF BM14
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 1.6 50 89.8 0.068 29.34 3 63103 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 48.5 0.23 3.67 2.2 1693
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 Native Pyridoxal Kinase from Entamoeba histolytica 1.6 50 59902 3160 89.63 0.1888 0.18722 0.1971 0.21894 0.2254 RANDOM 26.471
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] -0.58 0.6 0.27 -1.51 -0.08 1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.141 r_dihedral_angle_4_deg 16.817 r_dihedral_angle_3_deg 12.378 r_long_range_B_other 10.923 r_long_range_B_refined 10.885 r_scangle_other 9.624 r_scbond_it 8.117 r_scbond_other 8.116 r_dihedral_angle_1_deg 6.288 r_mcangle_it 5.511
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.141 r_dihedral_angle_4_deg 16.817 r_dihedral_angle_3_deg 12.378 r_long_range_B_other 10.923 r_long_range_B_refined 10.885 r_scangle_other 9.624 r_scbond_it 8.117 r_scbond_other 8.116 r_dihedral_angle_1_deg 6.288 r_mcangle_it 5.511 r_mcangle_other 5.51 r_mcbond_it 4.72 r_mcbond_other 4.718 r_angle_refined_deg 1.548 r_angle_other_deg 1.267 r_chiral_restr 0.11 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.005 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 4426 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 58
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling