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Structure of bifunctional TcDHFR-TS in complex with MTX
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H2Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 295 17% 2-METHYL-2,4-PENTANEDIOL, 10% PEG 4000, 0.1M POTASSIUM CITRATE, PH 6.0, , VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 4.05 69.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.05 α = 90 b = 121.05 β = 90 c = 260.76 γ = 90
Symmetry Space Group I 41 2 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 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 0.9998 APS 17-ID
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 3.3 19.78 97.5 0.01 0.01 9.6 5.1 14555 14555 1 87
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 3.3 3.42 99.5 0.433 3.2 5.3 1601
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2H2Q 3.3 19.78 13809 13809 738 97.47 0.20833 0.20626 0.1985 0.24901 0.2414 RANDOM 90.8
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] 0.03 0.03 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.899 r_dihedral_angle_3_deg 20.152 r_dihedral_angle_4_deg 15.737 r_dihedral_angle_1_deg 5.899 r_scangle_it 1.466 r_angle_refined_deg 1.322 r_scbond_it 0.811 r_mcangle_it 0.774 r_mcbond_it 0.428 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.899 r_dihedral_angle_3_deg 20.152 r_dihedral_angle_4_deg 15.737 r_dihedral_angle_1_deg 5.899 r_scangle_it 1.466 r_angle_refined_deg 1.322 r_scbond_it 0.811 r_mcangle_it 0.774 r_mcbond_it 0.428 r_nbtor_refined 0.313 r_nbd_refined 0.222 r_symmetry_hbond_refined 0.207 r_symmetry_vdw_refined 0.176 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4015 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling PHASER phasing