7XKY

Crystal structure of Methanocaldococcus jannaschii two-subunit Fumarate hydratase apo-protein complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH2970.2 M magnesium chloride hexahydrate, 0.1 M BIS-TRIS, pH 5.5, 25% w/v polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
2.346.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.949α = 90
b = 61.7β = 123.9
c = 83.88γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2016-07-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.9787ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.4669.6298.40.1240.99511.27.917961
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.462.590.5250.871

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 DIFFRACTIONSADTHROUGHOUT2.4652.131702293698.080.185860.183760.22394RANDOM31.066
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]
-2.55-0.19-2.042.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.37
r_dihedral_angle_4_deg20.892
r_dihedral_angle_3_deg16.674
r_dihedral_angle_1_deg6.812
r_long_range_B_refined6.728
r_long_range_B_other6.727
r_scangle_other5.25
r_mcangle_it3.924
r_mcangle_other3.924
r_scbond_it3.424
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.37
r_dihedral_angle_4_deg20.892
r_dihedral_angle_3_deg16.674
r_dihedral_angle_1_deg6.812
r_long_range_B_refined6.728
r_long_range_B_other6.727
r_scangle_other5.25
r_mcangle_it3.924
r_mcangle_other3.924
r_scbond_it3.424
r_scbond_other3.423
r_mcbond_it2.599
r_mcbond_other2.583
r_angle_refined_deg1.825
r_angle_other_deg1.345
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3502
Nucleic Acid Atoms
Solvent Atoms65
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
AutoSolphasing