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Crystal Structure Analysis of Glutathione-dependent formaldehyde-activating enzyme (Gfa)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X6M PDB ENTRY 1X6M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 (NH4)2SO4, HEPES, PEG400, 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.6 65.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.91 α = 90 b = 120.62 β = 97.68 c = 97.14 γ = 90
Symmetry Space Group P 1 21 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 MARRESEARCH two Au coated X-ray mirrors 2004-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 0.97 MPG/DESY, HAMBURG BW6
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.4 96.27 99.9 0.0867 0.1104 7.87 1.96 48095 48095 2.45 2.09
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.5 100 0.319 0.4849 2.16 1.97 5522
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB ENTRY 1X6M 2.4 75.16 2.09 44668 44668 3425 99.91 0.19889 0.19889 0.19507 0.1987 0.24784 0.2026 RANDOM 31.344
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] -0.28 -0.08 -0.22 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.998 r_dihedral_angle_3_deg 19.872 r_dihedral_angle_4_deg 19.367 r_dihedral_angle_1_deg 7.543 r_scangle_it 3.979 r_scbond_it 2.677 r_angle_refined_deg 2.095 r_mcangle_it 1.628 r_mcbond_it 0.934 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.998 r_dihedral_angle_3_deg 19.872 r_dihedral_angle_4_deg 19.367 r_dihedral_angle_1_deg 7.543 r_scangle_it 3.979 r_scbond_it 2.677 r_angle_refined_deg 2.095 r_mcangle_it 1.628 r_mcbond_it 0.934 r_nbtor_refined 0.3 r_symmetry_hbond_refined 0.284 r_symmetry_vdw_refined 0.238 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.2 r_chiral_restr 0.148 r_bond_refined_d 0.021 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5904 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 127
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling MOLREP phasing