8ZML | pdb_00008zml

Structure of TNIK with inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5D7A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.2 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 20% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.5251.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.889α = 90
b = 89.595β = 90
c = 97.577γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 R 4M2024-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL02U10.97918SSRFBL02U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.48965.99599.90.99917.29.225206
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.4892.590.777

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.48965.99525156131599.8850.2590.25560.2570.32630.323264.798
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]
1.7982.347-4.145
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.605
r_dihedral_angle_3_deg14.16
r_dihedral_angle_4_deg13.236
r_dihedral_angle_1_deg5.3
r_lrange_it4.509
r_lrange_other4.485
r_mcangle_it2.331
r_mcangle_other2.331
r_scangle_it1.439
r_scangle_other1.439
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.605
r_dihedral_angle_3_deg14.16
r_dihedral_angle_4_deg13.236
r_dihedral_angle_1_deg5.3
r_lrange_it4.509
r_lrange_other4.485
r_mcangle_it2.331
r_mcangle_other2.331
r_scangle_it1.439
r_scangle_other1.439
r_mcbond_other1.259
r_mcbond_it1.258
r_angle_refined_deg1.177
r_angle_other_deg0.985
r_scbond_it0.726
r_scbond_other0.726
r_nbd_refined0.155
r_symmetry_nbd_refined0.155
r_symmetry_nbd_other0.15
r_nbtor_refined0.143
r_xyhbond_nbd_refined0.124
r_nbd_other0.117
r_symmetry_xyhbond_nbd_refined0.111
r_symmetry_xyhbond_nbd_other0.088
r_symmetry_nbtor_other0.071
r_chiral_restr0.033
r_bond_refined_d0.002
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4843
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms82

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing