3QWA

Crystal structure of Saccharomyces cerevisiae Zeta-crystallin-like quinone oxidoreductase Zta1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QORPDB ENTRY 1QOR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP828925% polyethylene glycol 3350, 0.2M MgCl2, 0.1M Tris-HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K
Crystal Properties
Matthews coefficientSolvent content
2.2244.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.97α = 90
b = 87.313β = 90
c = 100.514γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.979SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12501000.08522.896.24522745227
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.071000.2767.736.24464

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 1QOR235.3242929228299.730.216010.214360.2468RANDOM19.604
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]
0.320.8-1.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.435
r_dihedral_angle_4_deg18.33
r_dihedral_angle_3_deg11.524
r_dihedral_angle_1_deg5.112
r_angle_refined_deg0.887
r_scangle_it0.863
r_scbond_it0.47
r_mcangle_it0.469
r_mcbond_it0.26
r_chiral_restr0.058
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.435
r_dihedral_angle_4_deg18.33
r_dihedral_angle_3_deg11.524
r_dihedral_angle_1_deg5.112
r_angle_refined_deg0.887
r_scangle_it0.863
r_scbond_it0.47
r_mcangle_it0.469
r_mcbond_it0.26
r_chiral_restr0.058
r_bond_refined_d0.006
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5190
Nucleic Acid Atoms
Solvent Atoms721
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling