7CAS

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


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 = 79.779α = 90
b = 100.219β = 90
c = 130.09γ = 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
12.28651000.0950.99919.313.924258
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)
12.282.40.6970.858

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 REPLACEMENTTHROUGHOUT7CAQ2.2865.0422983124799.970.221920.220.25812RANDOM45.784
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]
-0.060.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.103
r_dihedral_angle_4_deg19.53
r_dihedral_angle_3_deg17.63
r_dihedral_angle_1_deg7.256
r_long_range_B_refined6.231
r_long_range_B_other6.217
r_mcangle_it3.422
r_mcangle_other3.421
r_scangle_other3.253
r_mcbond_it1.972
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.103
r_dihedral_angle_4_deg19.53
r_dihedral_angle_3_deg17.63
r_dihedral_angle_1_deg7.256
r_long_range_B_refined6.231
r_long_range_B_other6.217
r_mcangle_it3.422
r_mcangle_other3.421
r_scangle_other3.253
r_mcbond_it1.972
r_mcbond_other1.966
r_scbond_it1.859
r_scbond_other1.849
r_angle_refined_deg1.01
r_angle_other_deg0.99
r_chiral_restr0.023
r_gen_planes_refined0.007
r_gen_planes_other0.004
r_bond_refined_d0.003
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 Atoms3406
Nucleic Acid Atoms
Solvent Atoms101
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing