4G9K

Structure of the Ndi1 protein from Saccharomyces cerevisiae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629334% PEG 400, 100 mM NaCl, 2% ethylene glycol, 5% glycerol, 50 mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.1961.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.12α = 90
b = 165.56β = 90
c = 70γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2006-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.98ESRFID23-1

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
12.74096.93571435714

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 REPLACEMENTTHROUGHOUT2.739.3227911140173.710.23540.23370.2677RANDOM68.936
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]
-2.38-17.8520.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.369
r_dihedral_angle_4_deg16.917
r_dihedral_angle_3_deg13.949
r_dihedral_angle_1_deg5.289
r_angle_refined_deg0.959
r_angle_other_deg0.787
r_chiral_restr0.058
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.369
r_dihedral_angle_4_deg16.917
r_dihedral_angle_3_deg13.949
r_dihedral_angle_1_deg5.289
r_angle_refined_deg0.959
r_angle_other_deg0.787
r_chiral_restr0.058
r_bond_refined_d0.005
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 Atoms18
Heterogen Atoms106

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing