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Pyridoxal Kinase of Entamoeba histolytica with PLP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4S1M PDB ENTRY 4S1M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 273 15%Peg4000, 0.1MTris pH 7.5, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.18 43.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.173 α = 90 b = 79.014 β = 90 c = 90.697 γ = 90
Symmetry Space Group P 21 2 21
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 99.8 0.067 55.27 14.6 74705 -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 99.9 0.89 2.34 13.6 3706
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 PDB ENTRY 4S1M 1.6 50 74705 3751 99.21 0.19609 0.19454 0.1988 0.22548 0.23 RANDOM 33.03
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] 2.64 -3.05 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.761 r_dihedral_angle_4_deg 16.006 r_dihedral_angle_3_deg 12.023 r_long_range_B_other 7.82 r_long_range_B_refined 7.789 r_dihedral_angle_1_deg 6.3 r_scangle_other 5.723 r_scbond_it 4.337 r_scbond_other 4.337 r_mcangle_it 3.398
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.761 r_dihedral_angle_4_deg 16.006 r_dihedral_angle_3_deg 12.023 r_long_range_B_other 7.82 r_long_range_B_refined 7.789 r_dihedral_angle_1_deg 6.3 r_scangle_other 5.723 r_scbond_it 4.337 r_scbond_other 4.337 r_mcangle_it 3.398 r_mcangle_other 3.398 r_mcbond_it 2.396 r_mcbond_other 2.395 r_angle_refined_deg 2.163 r_angle_other_deg 1.642 r_chiral_restr 0.138 r_bond_refined_d 0.022 r_gen_planes_refined 0.013 r_bond_other_d 0.01 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 261 Heterogen Atoms 34
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling