7CAQ

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X07 

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
2.5551.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.019α = 90
b = 100.439β = 90
c = 130.52γ = 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
11.6965.399.70.0720.99920.113.159466
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)
11.691.780.8160.8463

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 REPLACEMENTTHROUGHOUT1X071.6940.0456446294599.660.210790.208830.24766RANDOM32.915
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.957
r_dihedral_angle_4_deg20.15
r_dihedral_angle_3_deg16.885
r_long_range_B_refined7.532
r_long_range_B_other7.504
r_dihedral_angle_1_deg6.861
r_scangle_other5.801
r_mcangle_other4.18
r_mcangle_it4.179
r_scbond_other3.835
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.957
r_dihedral_angle_4_deg20.15
r_dihedral_angle_3_deg16.885
r_long_range_B_refined7.532
r_long_range_B_other7.504
r_dihedral_angle_1_deg6.861
r_scangle_other5.801
r_mcangle_other4.18
r_mcangle_it4.179
r_scbond_other3.835
r_scbond_it3.83
r_mcbond_it3.038
r_mcbond_other3.036
r_angle_refined_deg1.666
r_angle_other_deg1.345
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms3384
Nucleic Acid Atoms
Solvent Atoms298
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MrBUMPphasing