7VQB

Structure of MA1831 from Methanosarcina acetivorans in complex with farnesyl pyrophosphate and dimethylallyl diphosphate


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
2.5451.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.642α = 90
b = 80.778β = 103.56
c = 59.806γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON III2021-06-29MSINGLE 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
11.9633.0497.20.1090.1210.0510.9979.75.333955
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)
11.962.0161.10.6520.790.4330.6742.7

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 REPLACEMENTTHROUGHOUT7CAQ2.1133.0428321146899.940.15620.15380.2017RANDOM29.892
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]
2.11-0.45-0.31-1.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.472
r_dihedral_angle_4_deg19.505
r_dihedral_angle_3_deg17.609
r_dihedral_angle_1_deg6.656
r_angle_refined_deg1.532
r_angle_other_deg1.315
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.472
r_dihedral_angle_4_deg19.505
r_dihedral_angle_3_deg17.609
r_dihedral_angle_1_deg6.656
r_angle_refined_deg1.532
r_angle_other_deg1.315
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3378
Nucleic Acid Atoms
Solvent Atoms299
Heterogen Atoms93

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing