☰ Navigation Tabs
Avian respiratory complex ii with oxaloacetate and ubiquinone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NEK PDB ENTRY 1NEK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 278 50 G/L PEG-3350, 25 ML/L ISOPROPANOL,15 ML/L PEG-400 0.05 M NA-HEPES, 0.01 M TRIS-HCL, 0.0016 M MNCL2, 0.0013 M MGCL2, 0.0015 M NA-AZIDE, 0.00025 M NA-EDTA, OXALOACETATE , pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 3.5 64.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.008 α = 90 b = 84.398 β = 90 c = 289.496 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315 2004-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.19 99 87.5 0.119 11.9 4.5 79236 -3 34.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.19 2.27 49 0.27 2.61 2
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 (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 1NEK 2.2 38.66 78719 78719 3842 89.2 0.175 0.175 0.1676 0.223 0.2144 RANDOM 46
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] 2.79 15.44 -18.23
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_scangle_it 4.27 c_scbond_it 3.33 c_mcangle_it 3.05 c_angle_deg 2.5 c_mcbond_it 2.13 c_improper_angle_d 1.72 c_bond_d 0.036 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_scangle_it 4.27 c_scbond_it 3.33 c_mcangle_it 3.05 c_angle_deg 2.5 c_mcbond_it 2.13 c_improper_angle_d 1.72 c_bond_d 0.036 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8507 Nucleic Acid Atoms Solvent Atoms 834 Heterogen Atoms 235
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement