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Crystal structure of the C-terminal domain of rat 10'formyltetrahydrofolate dehydrogenase in complex with NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BI9 PDB entry 1BI9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 288 1.4 M AMMONIUM SULPHATE, 0.1M TRIS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 259.4 α = 90 b = 194.5 β = 108.8 c = 97.3 γ = 90
Symmetry Space Group C 1 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 100 CCD MARMOSAIC 300 mm CCD 2005-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-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 2 50 97.3 0.136 0.136 5.8 4.8 299165 299165 19.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 85.3 0.552 0.552 1.7 3.1 26210
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 PDB entry 1BI9 2 50 299163 299163 14997 97.3 0.169 0.169 0.168 0.1707 0.19 0.1912 RANDOM 19.44
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] 0.24 0.62 -0.04 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.677 r_dihedral_angle_4_deg 22.935 r_dihedral_angle_3_deg 13.661 r_dihedral_angle_1_deg 6.375 r_scangle_it 2.727 r_scbond_it 1.764 r_angle_refined_deg 1.293 r_mcangle_it 0.988 r_mcbond_it 0.604 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.677 r_dihedral_angle_4_deg 22.935 r_dihedral_angle_3_deg 13.661 r_dihedral_angle_1_deg 6.375 r_scangle_it 2.727 r_scbond_it 1.764 r_angle_refined_deg 1.293 r_mcangle_it 0.988 r_mcbond_it 0.604 r_nbtor_refined 0.3 r_nbd_refined 0.189 r_symmetry_vdw_refined 0.146 r_xyhbond_nbd_refined 0.124 r_symmetry_hbond_refined 0.104 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 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 15296 Nucleic Acid Atoms Solvent Atoms 1844 Heterogen Atoms 360
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing