3VR8

Mitochondrial rhodoquinol-fumarate reductase from the parasitic nematode Ascaris suum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZOYPDB ENTRY 1ZOY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS8.429315% (w/v) PEG 3350, 100mM Tris-HCl pH 8.4, 200mM NaCl, 1mM sodium malonate, 0.06% (w/v) C12E8, 0.04% (w/v) C12M, MICRODIALYSIS, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.1360.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.707α = 90
b = 129.09β = 90
c = 221.167γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDBruker DIP-6040monochromator2004-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

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
12.85092.50.1177.98.88009379622-3
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)
12.82.8567.50.5171.262.7

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 1ZOY2.8148.567601140251000.234460.231160.29717RANDOM96.74
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]
-0.660.350.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.764
r_dihedral_angle_3_deg23.059
r_dihedral_angle_4_deg21.697
r_dihedral_angle_1_deg7.152
r_scangle_it2.444
r_angle_refined_deg1.699
r_scbond_it1.426
r_mcangle_it1.138
r_mcbond_it0.598
r_chiral_restr0.114
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.764
r_dihedral_angle_3_deg23.059
r_dihedral_angle_4_deg21.697
r_dihedral_angle_1_deg7.152
r_scangle_it2.444
r_angle_refined_deg1.699
r_scbond_it1.426
r_mcangle_it1.138
r_mcbond_it0.598
r_chiral_restr0.114
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17862
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms370

Software

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