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Crystal structure of NADH dehydrogenase subunit C (Tfu_2693) from THERMOBIFIDA FUSCA YX-ER1 at 2.65 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FUG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 277 1.0000M 1,6-Hexanediol, 0.0100M CoCl2, 0.1M Acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.85 56.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.264 α = 90 b = 69.264 β = 90 c = 114.21 γ = 90
Symmetry Space Group P 43 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) 2008-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
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 2.65 48.97 99.8 0.048 25.89 6.95 8611 -3 82.093
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.74 100 0.81 2.1
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 MR THROUGHOUT 2fug 2.65 48.97 8568 402 99.88 0.21 0.207 0.2139 0.259 0.2629 RANDOM 40.196
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] 1.75 1.75 -3.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.209 r_dihedral_angle_4_deg 11.895 r_dihedral_angle_3_deg 11.558 r_scangle_it 5.754 r_scbond_it 3.605 r_dihedral_angle_1_deg 2.987 r_mcangle_it 2.126 r_angle_refined_deg 1.41 r_mcbond_it 1.087 r_angle_other_deg 0.967
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.209 r_dihedral_angle_4_deg 11.895 r_dihedral_angle_3_deg 11.558 r_scangle_it 5.754 r_scbond_it 3.605 r_dihedral_angle_1_deg 2.987 r_mcangle_it 2.126 r_angle_refined_deg 1.41 r_mcbond_it 1.087 r_angle_other_deg 0.967 r_mcbond_other 0.174 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1222 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement PHENIX refinement MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing