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Crystal structure of formyltetrahydrofolate deformylase from Thermus thermophilus HB8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LOU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10 293 50% 2-methyl-2,4-pentanediol, 0.1M CAPS, pH 10.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.4 48.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.592 α = 90 b = 90.726 β = 90 c = 87.483 γ = 90
Symmetry Space Group P 21 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 CCD RIGAKU JUPITER 210 Toroidal Mirror 2008-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.00000 SPring-8 BL38B1
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 2.5 50 99.9 0.122 28.9 7.3 17794 17779 48.3
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 2.8 100 0.335 5.9 7.3
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 (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 3LOU 2.71 29.92 17171 17171 1689 96.5 0.208 0.208 0.2082 0.261 0.2614 RANDOM 36.7
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] 12.81 -8.31 -4.5
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.1 c_scangle_it 3.78 c_mcangle_it 3.19 c_scbond_it 2.36 c_mcbond_it 1.79 c_angle_deg 1.3 c_improper_angle_d 0.84 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.1 c_scangle_it 3.78 c_mcangle_it 3.19 c_scbond_it 2.36 c_mcbond_it 1.79 c_angle_deg 1.3 c_improper_angle_d 0.84 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4630 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms
Software Software Software Name Purpose BSS data collection AMoRE phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling