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Crystal Structure of Pyridoxal Kinase from Entamoeba histolytica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Crystal structure of pyridoxal kinase from Trypanosoma brucei
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 273 15%Peg4000, 0.1M Tris pH7.5, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.36 47.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.131 α = 90 b = 91.111 β = 99.64 c = 76.777 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 2014-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.976 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 1.65 50 99.1 0.044 33.7 4.1 71764 -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 1.65 1.68 90.8 0.48 1.98 3.1 3287
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 Crystal structure of pyridoxal kinase from Trypanosoma brucei 1.64 50 71764 3612 98.56 0.17474 0.17351 0.1836 0.19756 0.2066 RANDOM 29.705
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] -0.71 0.42 0.65 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.668 r_dihedral_angle_4_deg 19.618 r_dihedral_angle_3_deg 12.368 r_long_range_B_other 6.809 r_long_range_B_refined 6.801 r_dihedral_angle_1_deg 6.427 r_scangle_other 5.119 r_scbond_it 3.508 r_scbond_other 3.508 r_mcangle_other 3.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.668 r_dihedral_angle_4_deg 19.618 r_dihedral_angle_3_deg 12.368 r_long_range_B_other 6.809 r_long_range_B_refined 6.801 r_dihedral_angle_1_deg 6.427 r_scangle_other 5.119 r_scbond_it 3.508 r_scbond_other 3.508 r_mcangle_other 3.257 r_mcangle_it 3.256 r_mcbond_it 2.331 r_mcbond_other 2.331 r_angle_refined_deg 1.769 r_angle_other_deg 1.513 r_chiral_restr 0.106 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.009 r_gen_planes_other 0.007 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 4333 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 2
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling