8TFO

Structure of MKvar


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2R42 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.4293Protein bound to mevalonate at about 3 mg/mL was set up in 150 nL plus 150 nL drops over 50 microlitres of reservoir which contained: 0.126 M calcium acetate, 24.9 v/v PEG 400, 0.09 M sodium HEPES pH 8.4 with 10 mM taurine
Crystal Properties
Matthews coefficientSolvent content
2.0840.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.081α = 90
b = 80.705β = 90
c = 207.467γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2020-11-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.953723Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
1245.199.80.2920.0570.99911.827.152511
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0597.54.6560.90.623126.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE244.09152296259899.9790.210.20790.247141.413
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]
2.5391.818-4.357
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.353
r_dihedral_angle_3_deg15.159
r_dihedral_angle_2_deg9.415
r_lrange_other8.847
r_lrange_it8.842
r_dihedral_angle_1_deg6.357
r_scangle_it5.897
r_scangle_other5.896
r_mcangle_it4.712
r_mcangle_other4.712
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.353
r_dihedral_angle_3_deg15.159
r_dihedral_angle_2_deg9.415
r_lrange_other8.847
r_lrange_it8.842
r_dihedral_angle_1_deg6.357
r_scangle_it5.897
r_scangle_other5.896
r_mcangle_it4.712
r_mcangle_other4.712
r_scbond_it3.781
r_scbond_other3.78
r_mcbond_it3.108
r_mcbond_other3.108
r_angle_refined_deg1.262
r_angle_other_deg0.431
r_nbd_other0.213
r_nbd_refined0.206
r_symmetry_xyhbond_nbd_refined0.193
r_symmetry_nbd_other0.192
r_nbtor_refined0.168
r_xyhbond_nbd_refined0.159
r_symmetry_nbd_refined0.121
r_ncsr_local_group_10.116
r_symmetry_nbtor_other0.076
r_symmetry_metal_ion_refined0.073
r_symmetry_xyhbond_nbd_other0.067
r_chiral_restr0.058
r_xyhbond_nbd_other0.02
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5885
Nucleic Acid Atoms
Solvent Atoms151
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing