7VQ9

Structure of MA1831 from Methanosarcina acetivorans in complex with farnesyl thiopyrophosphate and isopentyl S-thiolodiphosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7CAQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82981.5M ammonium sulfate, 0.1M Tris (pH 8.0), 12% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.5752.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.899α = 90
b = 81.308β = 103.46
c = 60.023γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON III2021-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1LIQUID ANODEBRUKER METALJET1.34138

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.8735.8898.70.0550.0590.020.99920.87.441757
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.871.92830.260.3050.1560.9353.4

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 REPLACEMENTTHROUGHOUT7CAQ1.8935.8837927205295.380.14440.14220.185RANDOM23.398
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]
0.9-0.06-0.06-0.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.833
r_dihedral_angle_4_deg21.783
r_dihedral_angle_3_deg15.322
r_dihedral_angle_1_deg6.217
r_angle_refined_deg1.7
r_angle_other_deg1.403
r_chiral_restr0.09
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.833
r_dihedral_angle_4_deg21.783
r_dihedral_angle_3_deg15.322
r_dihedral_angle_1_deg6.217
r_angle_refined_deg1.7
r_angle_other_deg1.403
r_chiral_restr0.09
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3353
Nucleic Acid Atoms
Solvent Atoms401
Heterogen Atoms98

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing