8TEB

Structure of MKbur


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherMR from other structure done on same project

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293Sitting drops were set up with 150 nL plus 150 nL volumes over 50 microlitre wells; the crystallisation reservoir contained: 20% PEG 8000, 200 mM MgCl2, 100 mM tris pH 8.5 and 3% trehalose. The protein concentration was about 24 mg/mL
Crystal Properties
Matthews coefficientSolvent content
2.4449.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.338α = 90
b = 93.034β = 90.045
c = 90.389γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2022-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.9537Australian 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
12.246.599.50.1130.0460.99813.7732249
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)
12.22.2697.90.7170.2850.8492.87

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-VALUE2.246.532228150399.3680.1880.18570.238234.021
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]
0.669-0.8620.992-1.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg17.826
r_dihedral_angle_6_deg16.965
r_dihedral_angle_3_deg15.888
r_lrange_it8.512
r_lrange_other8.512
r_dihedral_angle_1_deg6.671
r_scangle_it6.09
r_scangle_other6.089
r_mcangle_it4.358
r_mcangle_other4.358
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg17.826
r_dihedral_angle_6_deg16.965
r_dihedral_angle_3_deg15.888
r_lrange_it8.512
r_lrange_other8.512
r_dihedral_angle_1_deg6.671
r_scangle_it6.09
r_scangle_other6.089
r_mcangle_it4.358
r_mcangle_other4.358
r_scbond_it3.942
r_scbond_other3.941
r_mcbond_it2.94
r_mcbond_other2.939
r_angle_refined_deg1.289
r_angle_other_deg0.437
r_nbd_refined0.209
r_symmetry_nbd_other0.191
r_nbtor_refined0.169
r_symmetry_nbd_refined0.159
r_xyhbond_nbd_refined0.148
r_nbd_other0.137
r_ncsr_local_group_10.088
r_symmetry_nbtor_other0.079
r_chiral_restr0.06
r_symmetry_xyhbond_nbd_refined0.025
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4407
Nucleic Acid Atoms
Solvent Atoms202
Heterogen Atoms7

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing