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The human methylenetetrahydrofolate dehydrogenase/cyclohydrolase (FolD) complexed with NADP and inhibitor LY345899
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DIB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 293 PEG 3350, GLYCEROL, SODIUM CITRATE, AMMONIUM ACETATE, pH 5.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 20K.
Crystal Properties Matthews coefficient Solvent content 2.2 44.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.49 α = 90 b = 136.37 β = 90 c = 61.38 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 IMAGE PLATE RIGAKU RAXIS IIC M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.7 20 97.1 0.1 3 5 15688 15688 -3 -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 2.7 2.74 95.9 0.332 5
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 FOURIER SYNTHESIS THROUGHOUT 1DIB 2.7 19.6 13706 1548 94.37 0.18592 0.17905 0.1848 0.24725 0.2471 RANDOM 24.615
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] -0.22 0.55 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.224 r_dihedral_angle_4_deg 16.927 r_dihedral_angle_3_deg 15.587 r_dihedral_angle_1_deg 5.975 r_long_range_B_refined 4.393 r_long_range_B_other 4.377 r_scangle_other 2.614 r_mcangle_other 2.181 r_mcangle_it 2.18 r_angle_refined_deg 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.224 r_dihedral_angle_4_deg 16.927 r_dihedral_angle_3_deg 15.587 r_dihedral_angle_1_deg 5.975 r_long_range_B_refined 4.393 r_long_range_B_other 4.377 r_scangle_other 2.614 r_mcangle_other 2.181 r_mcangle_it 2.18 r_angle_refined_deg 1.55 r_scbond_other 1.532 r_scbond_it 1.531 r_mcbond_it 1.292 r_mcbond_other 1.29 r_angle_other_deg 0.963 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4412 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing