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Plasmodium vivax ethanolamine kinase Pv091845
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CK0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 1.4M Na Citrate, 0.1M Hepes pH7.5, 2mM TCEP, 1mM MgCl2, 4mm CaCl2, 4mM ethanolamine chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.77 55.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.031 α = 90 b = 172.702 β = 110.72 c = 93.353 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 CCD MAR CCD 165 mm 2007-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-BM 1.000 APS 17-BM
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 2.4 50 95.1 0.058 20.28 3.4 85067 85067
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) 2.4 2.49 57.4 0.262 2 1.4 5104
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2CK0 2.407 24.93 80452 80452 4237 96.1 0.2331 0.2331 0.23011 0.2226 0.28974 0.2792 RANDOM 61.755
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] -0.56 1.16 1.83 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.761 r_dihedral_angle_4_deg 18.294 r_dihedral_angle_3_deg 15.331 r_dihedral_angle_1_deg 5.748 r_scangle_it 3.632 r_scbond_it 2.523 r_mcangle_it 1.67 r_mcbond_it 1.349 r_angle_refined_deg 1.342 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.761 r_dihedral_angle_4_deg 18.294 r_dihedral_angle_3_deg 15.331 r_dihedral_angle_1_deg 5.748 r_scangle_it 3.632 r_scbond_it 2.523 r_mcangle_it 1.67 r_mcbond_it 1.349 r_angle_refined_deg 1.342 r_nbtor_refined 0.299 r_symmetry_hbond_refined 0.195 r_nbd_refined 0.181 r_symmetry_vdw_refined 0.151 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.093 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12177 Nucleic Acid Atoms Solvent Atoms 456 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction SCALEPACK data scaling PHASER phasing