7CAR

Versatile cis-prenyltransferase MM_0014 from Methanosarcina mazei (crystal type: free+IPP)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2934 mM cobalt (II) chloride, 4 mM nickel (II) chloride, 4 mM cadmium chloride, 4 mM magnesium chloride, 0.075 M HEPES, pH7.5, 9% PEG 3350, 25% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.5351.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.94α = 90
b = 100.42β = 90
c = 129.56γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702017-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.000Photon FactoryAR-NW12A

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
11.9864.899.80.0710.99922.11436516
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)
11.982.090.660.856

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 REPLACEMENTTHROUGHOUT7CAQ1.9839.7234644184799.690.221450.219530.25878RANDOM44.366
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.006
r_dihedral_angle_4_deg26.475
r_dihedral_angle_3_deg17.557
r_long_range_B_other9.308
r_long_range_B_refined9.303
r_scangle_other6.652
r_dihedral_angle_1_deg6.548
r_mcangle_it5.175
r_mcangle_other5.175
r_scbond_it4.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.006
r_dihedral_angle_4_deg26.475
r_dihedral_angle_3_deg17.557
r_long_range_B_other9.308
r_long_range_B_refined9.303
r_scangle_other6.652
r_dihedral_angle_1_deg6.548
r_mcangle_it5.175
r_mcangle_other5.175
r_scbond_it4.312
r_scbond_other4.312
r_mcbond_it3.671
r_mcbond_other3.668
r_angle_other_deg2.239
r_angle_refined_deg1.504
r_chiral_restr0.069
r_bond_other_d0.034
r_gen_planes_other0.01
r_bond_refined_d0.009
r_gen_planes_refined0.007
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 Atoms3356
Nucleic Acid Atoms
Solvent Atoms147
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing