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2.35 Angstrom Crystal Structure of Conserved Hypothetical Protein from Toxoplasma gondii ME49.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PD0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 Protein: 7.0mg/mL, 0.5M Sodium cloride, Tris-HCl pH 8.3;
Screen: JCSG+ (F11), 1M Succinic acid pH 7.0, 0.1M HEPES pH 7.0, 1.0% (w/v) PEG MME 2000;
Cryo: Screen solution : 50% Sucrose, 1:1 (v/v), VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.15 42.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.599 α = 90 b = 87.216 β = 90 c = 112.122 γ = 90
Symmetry Space Group P 21 21 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 CCD MARMOSAIC 225 mm CCD Beryllium lenses 2011-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 30 100 0.066 27.6 7.3 20165 20165 -3 58.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.39 100 0.557 3.9 7.2 983
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 2PD0 2.35 29.4 19076 19076 1026 99.96 0.20509 0.20509 0.20232 0.2056 0.25826 0.2584 RANDOM 53.823
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] -0.51 1.53 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.658 r_dihedral_angle_3_deg 11.99 r_dihedral_angle_4_deg 10.074 r_scangle_it 4.433 r_scbond_it 3.053 r_dihedral_angle_1_deg 2.609 r_mcangle_it 2.223 r_angle_refined_deg 1.471 r_mcbond_it 1.235 r_angle_other_deg 0.851
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.658 r_dihedral_angle_3_deg 11.99 r_dihedral_angle_4_deg 10.074 r_scangle_it 4.433 r_scbond_it 3.053 r_dihedral_angle_1_deg 2.609 r_mcangle_it 2.223 r_angle_refined_deg 1.471 r_mcbond_it 1.235 r_angle_other_deg 0.851 r_mcbond_other 0.289 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3172 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection PHENIX model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing