6VXR

Structure of Maternal embryonic leucine zipper kinase bound to LDSM276


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5IH9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29325% PEG 1,500
Crystal Properties
Matthews coefficientSolvent content
2.3748.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.124α = 90
b = 70.159β = 90
c = 102.067γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-06-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.96858DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
1219.8599.90.0950.0990.0280.99913.612.825981
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.051002.6792.7880.7640.50613.2

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 REPLACEMENTTHROUGHOUT5IH92.119.8421334112899.80.22060.2190.2483RANDOM51.597
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]
2.73-0.82-1.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.566
r_dihedral_angle_4_deg21.194
r_dihedral_angle_3_deg13.891
r_dihedral_angle_1_deg6.253
r_angle_refined_deg1.215
r_angle_other_deg1.173
r_chiral_restr0.049
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.566
r_dihedral_angle_4_deg21.194
r_dihedral_angle_3_deg13.891
r_dihedral_angle_1_deg6.253
r_angle_refined_deg1.215
r_angle_other_deg1.173
r_chiral_restr0.049
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2430
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms32

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction