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Crystal Structure of inactivated form of CDPK1 from toxoplasma gondii, TGME49.101440
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HZT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 20% PEG 3350, 0.2 M KF, 2mM AMPPNP, 4 mM MgCl2, 6.25 mM TCEP, 30% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.97 37.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.01 α = 90 b = 72.912 β = 96.26 c = 65.018 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 RIGAKU SATURN A200 2009-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.3 50 99.5 0.059 0.048 8 3.5 20008 19908 56.66
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-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3hzt 2.3 19.97 19889 19811 1009 99.61 0.1979 0.2365 0.2284 RANDOM 55.17
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] 0.2685 0.5026 -0.0315 -0.237
RMS Deviations Key Refinement Restraint Deviation o_angle_deg 1.09 o_bond_d 0.01 o_bond_d_na o_bond_d_prot o_angle_d o_angle_d_na o_angle_d_prot o_angle_deg_na o_angle_deg_prot o_dihedral_angle_d
RMS Deviations Key Refinement Restraint Deviation o_angle_deg 1.09 o_bond_d 0.01 o_bond_d_na o_bond_d_prot o_angle_d o_angle_d_na o_angle_d_prot o_angle_deg_na o_angle_deg_prot o_dihedral_angle_d o_dihedral_angle_d_na o_dihedral_angle_d_prot o_improper_angle_d o_improper_angle_d_na o_improper_angle_d_prot o_mcbond_it o_mcangle_it o_scbond_it o_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3545 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 31
Software Software Software Name Purpose BUSTER refinement SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling DENZO data reduction