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Crystal structure of a tungsten formylmethanofuran dehydrogenase subunit e (fmde)-like protein (syn_00638) from syntrophus aciditrophicus at 1.90 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.01M NiCl2, 20.0% PEG MME 2000, 0.1M Tris-HCl pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.33 47.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.356 α = 90 b = 54.356 β = 90 c = 136.719 γ = 90
Symmetry Space Group P 41 21 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) 2008-04-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97817 SSRL BL11-1
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 1.9 29.386 99.9 0.078 0.078 6.8 7 16955 30.675
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 1.9 1.95 99.9 0.011 1.134 0.7 7.1 1208
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.9 29.386 16902 855 99.9 0.235 0.233 0.2362 0.268 0.2694 RANDOM 35.2
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] 1.73 1.73 -3.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.474 r_dihedral_angle_4_deg 21.608 r_dihedral_angle_3_deg 14.661 r_dihedral_angle_1_deg 6.4 r_mcangle_it 1.913 r_angle_refined_deg 1.604 r_scangle_it 1.576 r_mcbond_it 1.214 r_scbond_it 1.086 r_angle_other_deg 1.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.474 r_dihedral_angle_4_deg 21.608 r_dihedral_angle_3_deg 14.661 r_dihedral_angle_1_deg 6.4 r_mcangle_it 1.913 r_angle_refined_deg 1.604 r_scangle_it 1.576 r_mcbond_it 1.214 r_scbond_it 1.086 r_angle_other_deg 1.031 r_mcbond_other 0.264 r_symmetry_vdw_other 0.226 r_nbd_refined 0.2 r_nbd_other 0.196 r_nbtor_refined 0.182 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.175 r_symmetry_vdw_refined 0.114 r_chiral_restr 0.088 r_nbtor_other 0.087 r_bond_refined_d 0.019 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1388 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SHELXD phasing autoSHARP phasing