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T. Gondii bradyzoite-specific LDH (LDH2) in complex with NAD and OXQ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SOW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 293 14% PEG 5K, .6M Magnesium Acetate, .1M Sodium Acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.04 59.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.949 α = 90 b = 140.949 β = 90 c = 75.01 γ = 120
Symmetry Space Group P 3 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 CCD ADSC QUANTUM 315 2008-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 .97946 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 47.35 98.19 36662 35999
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1SOW 2.3 47.35 36662 35999 1901 98.19 0.16859 0.16568 0.22253 0.1611 RANDOM 33.096
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.297 r_dihedral_angle_4_deg 17.89 r_dihedral_angle_3_deg 16.799 r_dihedral_angle_1_deg 6.609 r_scangle_it 5.956 r_scbond_it 4.262 r_mcangle_it 2.424 r_angle_refined_deg 1.872 r_mcbond_it 1.679 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.297 r_dihedral_angle_4_deg 17.89 r_dihedral_angle_3_deg 16.799 r_dihedral_angle_1_deg 6.609 r_scangle_it 5.956 r_scbond_it 4.262 r_mcangle_it 2.424 r_angle_refined_deg 1.872 r_mcbond_it 1.679 r_nbtor_refined 0.315 r_nbd_refined 0.291 r_xyhbond_nbd_refined 0.198 r_symmetry_vdw_refined 0.193 r_chiral_restr 0.124 r_symmetry_hbond_refined 0.078 r_bond_refined_d 0.019 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4898 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling EPMR phasing