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Crystal structure of choline kinase from Cryptosporidium parvum Iowa II, cgd3_2030
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FI8 PDB entry 3FI8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 18.5% P3350, 0.2 M KNa-Tartrate, 2 mM Decamethonium bromide, 2 mM TCEP, 2 mM ADP and 4 mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.091 α = 90 b = 67.957 β = 116.54 c = 92.109 γ = 90
Symmetry Space Group C 1 2 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 RIGAKU RAXIS IV++ 2010-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
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 2.35 20 99.6 0.1382 7.68 3.68 39440 39277
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) 2.35 2.45 99.8 0.4979 2.14 3.65 4578
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 3FI8 2.35 19.72 37308 1964 100 0.24733 0.24498 0.2457 0.29108 0.2883 RANDOM 25.144
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] 2.78 1.56 -1.7 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.93 r_dihedral_angle_3_deg 13.577 r_dihedral_angle_4_deg 13.092 r_dihedral_angle_1_deg 3.91 r_angle_refined_deg 0.659 r_scangle_it 0.65 r_mcangle_it 0.4 r_scbond_it 0.376 r_mcbond_it 0.217 r_chiral_restr 0.047
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.93 r_dihedral_angle_3_deg 13.577 r_dihedral_angle_4_deg 13.092 r_dihedral_angle_1_deg 3.91 r_angle_refined_deg 0.659 r_scangle_it 0.65 r_mcangle_it 0.4 r_scbond_it 0.376 r_mcbond_it 0.217 r_chiral_restr 0.047 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5952 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 126
Software Software Software Name Purpose CrystalClear data collection BALBES phasing REFMAC refinement XDS data reduction XDS data scaling