7HNJ

PanDDA analysis group deposition -- Crystal Structure of TRIM21 in complex with Z1162778919


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VOK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82934 % PEG 400, 2 M AmmSO4, 0.1 M HEPES pH 8
Crystal Properties
Matthews coefficientSolvent content
2.4149.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.373α = 90
b = 95.373β = 90
c = 45.819γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 9M2024-07-03SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92134DiamondI04-1

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
11.4367.441000.2780.2890.0810.99713.812.838158
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)
11.431.461009.999103.7270.3569.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.4367.4436308184999.980.17060.16930.1955RANDOM20.221
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]
-0.11-0.110.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.027
r_dihedral_angle_4_deg21.283
r_dihedral_angle_3_deg12.692
r_dihedral_angle_1_deg7.151
r_mcangle_it2.711
r_angle_refined_deg1.754
r_mcbond_it1.72
r_mcbond_other1.71
r_angle_other_deg1.434
r_chiral_restr0.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.027
r_dihedral_angle_4_deg21.283
r_dihedral_angle_3_deg12.692
r_dihedral_angle_1_deg7.151
r_mcangle_it2.711
r_angle_refined_deg1.754
r_mcbond_it1.72
r_mcbond_other1.71
r_angle_other_deg1.434
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1493
Nucleic Acid Atoms
Solvent Atoms139
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing