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Crystal structure of the glutathione-dependent formaldehyde-activating enzyme (Gfa)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 (NH4)2SO4, PEG 400, HEPES, 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 = 53.36 α = 90 b = 118.86 β = 97.48 c = 95.99 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 2004-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.97980 SLS X06SA
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 2.35 74.33 99.8 0.077 0.0889 8.66 1.95 49354 49354 2.08 2.08
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 2.35 2.45 100 0.383 0.4846 2.17 1.96 5774
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 Se-SAD THROUGHOUT 2.35 74.29 2.08 45898 45898 3455 100 0.19348 0.19348 0.18923 0.1891 0.25022 0.2507 RANDOM 38.04
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] -0.93 -0.59 -1.48 2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.863 r_dihedral_angle_4_deg 21.991 r_dihedral_angle_3_deg 19.624 r_dihedral_angle_1_deg 7.133 r_scangle_it 4.482 r_scbond_it 2.874 r_angle_refined_deg 1.987 r_mcangle_it 1.74 r_mcbond_it 1.005 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.863 r_dihedral_angle_4_deg 21.991 r_dihedral_angle_3_deg 19.624 r_dihedral_angle_1_deg 7.133 r_scangle_it 4.482 r_scbond_it 2.874 r_angle_refined_deg 1.987 r_mcangle_it 1.74 r_mcbond_it 1.005 r_nbtor_refined 0.308 r_nbd_refined 0.224 r_symmetry_vdw_refined 0.199 r_xyhbond_nbd_refined 0.194 r_symmetry_hbond_refined 0.172 r_chiral_restr 0.139 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other 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 5904 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling SOLVE phasing