4GAV

Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with quinone


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629350 mM MES, 34% PEG 400, 100 mM NaCl, 2% Ethylene Glycol, 5% glycerol, 3 mM UQ2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8857.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.589α = 90
b = 111.926β = 90
c = 165.525γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2010-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.98DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
134098.624820

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT339.524779126898.560.24140.23990.2684RANDOM101.997
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]
-0.04-0.060.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.522
r_dihedral_angle_3_deg14.646
r_dihedral_angle_4_deg14.279
r_dihedral_angle_1_deg5.23
r_angle_refined_deg0.958
r_angle_other_deg0.793
r_chiral_restr0.055
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.522
r_dihedral_angle_3_deg14.646
r_dihedral_angle_4_deg14.279
r_dihedral_angle_1_deg5.23
r_angle_refined_deg0.958
r_angle_other_deg0.793
r_chiral_restr0.055
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7334
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms152

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing