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Human GAR Tfase complex structure with polyglutamated 10-(trifluoroacetyl)-5,10-dideazaacyclic-5,6,7,8-tetrahydrofolic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NJS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 MPD, Calcium cloride, MES, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.71 73.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.099 α = 90 b = 126.099 β = 90 c = 94.269 γ = 120
Symmetry Space Group P 31 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 ADSC QUANTUM 9 mirror 2002-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9540 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.27 31.47 98.1 0.064 15.76 2.84 37921 37921 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.27 2.32 98.6 0.344 2.8 2.72
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 1NJS 2.3 31.47 36318 36318 1814 95.73 0.237 0.237 0.23555 0.2278 0.26553 0.256 RANDOM 21.005
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] -0.23 -0.11 -0.23 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.795 r_scangle_it 3.153 r_scbond_it 1.909 r_angle_refined_deg 1.294 r_mcangle_it 0.997 r_mcbond_it 0.514 r_symmetry_hbond_refined 0.449 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.201 r_xyhbond_nbd_refined 0.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.795 r_scangle_it 3.153 r_scbond_it 1.909 r_angle_refined_deg 1.294 r_mcangle_it 0.997 r_mcbond_it 0.514 r_symmetry_hbond_refined 0.449 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.201 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_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 3014 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 96
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling AMoRE phasing REFMAC refinement HKL-2000 data reduction