6QRJ

Crystal structure of ShkA full-length in complex with AMPPNP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4Q20 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52980.2 M DL-Serine, 0.1M Sodium HEPES pH 7.5, MOPS (acid), 40% v/v ethylene glycol and 20% w/v PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.6954.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.504α = 90
b = 64.504β = 90
c = 260.209γ = 90
Symmetry
Space GroupP 43 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.00004SLSX06DA

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
12.6420990.010.0311712.7170581.05
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)
12.642.899.20.010.030.4820.867.027

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 REPLACEMENTTHROUGHOUT4q202.65201601384399.520.21960.21660.2747RANDOM82.808
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]
0.350.35-0.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.129
r_dihedral_angle_3_deg21.481
r_dihedral_angle_4_deg18.966
r_dihedral_angle_1_deg9.621
r_angle_refined_deg1.925
r_angle_other_deg1.302
r_chiral_restr0.229
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.129
r_dihedral_angle_3_deg21.481
r_dihedral_angle_4_deg18.966
r_dihedral_angle_1_deg9.621
r_angle_refined_deg1.925
r_angle_other_deg1.302
r_chiral_restr0.229
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.004
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3383
Nucleic Acid Atoms
Solvent Atoms11
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing