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Avian Respiratory Complex II with Malonate Bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YQ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 50 G/L PEG-3350, 25 ML/L
ISOPROPANOL, 15 ML/L PEG-400 0.05 M NA-HEPES, 0.01 M TRIS-HCL, 0.0005 M MALONATE,
0.0005 M MNCL2, 0.0013 M MGCL2, 0.0015 M NA-AZIDE, 0.00025 M NA-EDTA., pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.51 64.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.52 α = 90 b = 84.118 β = 90 c = 292.212 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 2004-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.1000 ALS 5.0.2
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 2.29 60 78.6 0.158 7 2.4 63148 63148 -999 -3 52.7
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 2.29 2.33 18.5 0.545 1.2 1.5 724
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 rigid body refinement of previous THROUGHOUT 1YQ3 2.4 50.74 59635 59635 2908 86.3 0.229 0.229 0.226 0.2176 0.279 0.2714 RANDOM 59.8
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] 6.89 5.97 -12.86
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_scangle_it 4.27 c_mcangle_it 3.39 c_scbond_it 3.1 c_mcbond_it 2.13 c_angle_deg 1.6 c_improper_angle_d 0.9 c_bond_d 0.011 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_scangle_it 4.27 c_mcangle_it 3.39 c_scbond_it 3.1 c_mcbond_it 2.13 c_angle_deg 1.6 c_improper_angle_d 0.9 c_bond_d 0.011 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 8500 Nucleic Acid Atoms Solvent Atoms 580 Heterogen Atoms 222
Software Software Software Name Purpose CNS refinement Blu-Ice data collection DENZO data reduction SCALEPACK data scaling CNS phasing