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The structure of human glycinamide ribonucleotide transformylase in complex with 10R-methylthio-DDATHF.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MEO PDB ENTRY 1MEO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 298 0.1 M phosphate/citrate buffer, 1.5-2.0 M ammonium sulfate at p.H 4.2. 25% Glycerol added as , VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.47 72.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.124 α = 90 b = 78.124 β = 90 c = 230.048 γ = 120
Symmetry Space Group P 65 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing), single crystal Si(111) bent monochromator
(horizontal focusing) 2007-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.9795 SSRL BL11-1
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 1.7 67.73 99.9 0.042 38.3 7.8 46588 28.9
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) 1 1.7 1.76 99.7 0.696 38.3 10 4512
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1MEO 1.702 67.73 46452 2349 99.8 0.2 0.2 0.1997 0.215 0.2111 RANDOM 29.368
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] -0.37 -0.18 -0.37 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.691 r_dihedral_angle_4_deg 18.714 r_dihedral_angle_3_deg 13.108 r_sphericity_free 10.533 r_sphericity_bonded 7.212 r_dihedral_angle_1_deg 5.668 r_scangle_it 4.784 r_scbond_it 3.229 r_mcangle_it 2.385 r_rigid_bond_restr 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.691 r_dihedral_angle_4_deg 18.714 r_dihedral_angle_3_deg 13.108 r_sphericity_free 10.533 r_sphericity_bonded 7.212 r_dihedral_angle_1_deg 5.668 r_scangle_it 4.784 r_scbond_it 3.229 r_mcangle_it 2.385 r_rigid_bond_restr 1.71 r_angle_refined_deg 1.676 r_mcbond_it 1.568 r_angle_other_deg 1.131 r_mcbond_other 1.074 r_chiral_restr 0.1 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1554 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling