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Crystal structure of a complex of pterin-4a-carbinolamine dehydratase from Toxoplasma gondii with 7,8-dihydrobiopterin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V6S PDB ENTRY 2V6S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.6 0.4 M POTASSIUM-SODIUM TARTRATE, pH 7.6
Crystal Properties Matthews coefficient Solvent content 3.82 67.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.51 α = 90 b = 119.51 β = 90 c = 49.928 γ = 90
Symmetry Space Group P 43 21 2
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 IMAGE PLATE OSMIC CONFOCAL OPTICS 2006-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 3.1 43 100 0.05 11.5 9.2 6969 3
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 3.1 3.27 100 0.47 1.6 9.4
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 2V6S 3.1 42.99 6591 341 99.9 0.19 0.187 0.1979 0.271 0.2672 RANDOM 79.11
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] 0.09 0.09 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.77 r_dihedral_angle_3_deg 22.207 r_dihedral_angle_4_deg 21.6 r_dihedral_angle_1_deg 11.436 r_scangle_it 3.617 r_scbond_it 2.283 r_angle_refined_deg 2.254 r_mcangle_it 1.592 r_mcbond_it 0.811 r_nbtor_refined 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.77 r_dihedral_angle_3_deg 22.207 r_dihedral_angle_4_deg 21.6 r_dihedral_angle_1_deg 11.436 r_scangle_it 3.617 r_scbond_it 2.283 r_angle_refined_deg 2.254 r_mcangle_it 1.592 r_mcbond_it 0.811 r_nbtor_refined 0.326 r_nbd_refined 0.286 r_symmetry_hbond_refined 0.259 r_symmetry_vdw_refined 0.237 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.143 r_bond_refined_d 0.022 r_gen_planes_refined 0.008 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1622 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing