8S00

CpKRS complexed with lysine and an inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherinternal model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293Protein buffer: 25 mM HEPES, 500 mM NaCl, 5% glycerol, 0.5 mM TCEP, pH 7, 30 mg/ml Reservoir: 0.2 M Li2SO4, 14-18% PEG3350, 0.1 M tris pH 7.4-7.8
Crystal Properties
Matthews coefficientSolvent content
2.5952.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.987α = 90
b = 121.761β = 90
c = 143.092γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2020-10-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97627DiamondI03

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
1256.081000.2230.090.9978.713.88686927.96
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)
122.041002.5161.0020.4941.214.1

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-VALUE256.0886793433399.9760.1840.18160.221933.101
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]
-1.8212.743-0.922
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.14
r_dihedral_angle_3_deg14.39
r_dihedral_angle_2_deg8.29
r_dihedral_angle_1_deg7.007
r_lrange_it6.529
r_lrange_other6.494
r_scangle_it5.529
r_scangle_other5.528
r_scbond_it3.717
r_scbond_other3.717
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.14
r_dihedral_angle_3_deg14.39
r_dihedral_angle_2_deg8.29
r_dihedral_angle_1_deg7.007
r_lrange_it6.529
r_lrange_other6.494
r_scangle_it5.529
r_scangle_other5.528
r_scbond_it3.717
r_scbond_other3.717
r_mcangle_it3.588
r_mcangle_other3.588
r_mcbond_it2.696
r_mcbond_other2.695
r_angle_refined_deg1.337
r_angle_other_deg0.463
r_nbd_other0.22
r_nbd_refined0.209
r_symmetry_nbd_other0.192
r_symmetry_xyhbond_nbd_refined0.186
r_nbtor_refined0.181
r_symmetry_nbd_refined0.178
r_xyhbond_nbd_refined0.164
r_symmetry_nbtor_other0.079
r_chiral_restr0.067
r_ncsr_local_group_10.063
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8118
Nucleic Acid Atoms
Solvent Atoms696
Heterogen Atoms92

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing