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Crystal structure of the Anaerobic DesB-Gallate complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WR8 DesB substrate-free form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.75 277 25% PEG8000, 0.1M SODIUM ACETATE, 0.1M HEPES-NAOH, pH 7.75, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.74 55.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.523 α = 90 b = 159.182 β = 90 c = 104.498 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315r 2010-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 2.4 53.2 99.9 0.122 16.58 8.77 40594 40553
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.52 100 4.28 9.02
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 (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 DesB substrate-free form 2.4 53.17 38540 38540 2029 100 0.188 0.188 0.185 0.1838 0.239 0.2346 RANDOM 28.43
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] -0.04 1.64 -1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.889 r_dihedral_angle_4_deg 18.069 r_dihedral_angle_3_deg 13.71 r_dihedral_angle_1_deg 5.85 r_scangle_it 3.184 r_scbond_it 1.904 r_angle_refined_deg 1.293 r_mcangle_it 1.102 r_mcbond_it 0.558 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.889 r_dihedral_angle_4_deg 18.069 r_dihedral_angle_3_deg 13.71 r_dihedral_angle_1_deg 5.85 r_scangle_it 3.184 r_scbond_it 1.904 r_angle_refined_deg 1.293 r_mcangle_it 1.102 r_mcbond_it 0.558 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6585 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 28
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling