☰ Navigation Tabs
High resolution structure of human glycinamide ribonucleotide transformylase in apo form.
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 cryoprotectant, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.47 72.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.028 α = 90 b = 78.028 β = 90 c = 230.841 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 225 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 1.52 67.57 99.7 0.043 41.4 9.5 64515
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 1.52 1.57 98.4 0.589 3 7.6
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 1.522 67.57 61124 3263 99.64 0.17385 0.17283 0.1744 0.19304 0.189 RANDOM 19.836
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] -0.45 -0.22 -0.45 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.614 r_dihedral_angle_4_deg 18.065 r_dihedral_angle_3_deg 12.49 r_scangle_it 6.09 r_dihedral_angle_1_deg 6.074 r_scbond_it 4.188 r_mcangle_it 3.044 r_mcbond_it 1.969 r_rigid_bond_restr 1.709 r_angle_refined_deg 1.636
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.614 r_dihedral_angle_4_deg 18.065 r_dihedral_angle_3_deg 12.49 r_scangle_it 6.09 r_dihedral_angle_1_deg 6.074 r_scbond_it 4.188 r_mcangle_it 3.044 r_mcbond_it 1.969 r_rigid_bond_restr 1.709 r_angle_refined_deg 1.636 r_angle_other_deg 0.974 r_mcbond_other 0.733 r_chiral_restr 0.098 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1554 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling