9GTG | pdb_00009gtg

RIPK1 in complex with AZ"902


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherInhouse

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29320 % PEG4000, 0.3 M NaCl, 0.1 M MES pH 6.5.
Crystal Properties
Matthews coefficientSolvent content
2.0640.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.084α = 90
b = 96.491β = 90
c = 129.002γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 200K2022-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.976MAX IVBioMAX

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.2577.2785.60.1090.1190.04696.724404
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.2552.39526.41.4591.5760.5917

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.2577.2723243116185.630.221180.217250.22730.294850.2933RANDOM71.063
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]
0.05-0.10.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.585
r_dihedral_angle_3_deg17.989
r_long_range_B_refined12.295
r_long_range_B_other12.292
r_scangle_other9.552
r_mcangle_it9.177
r_mcangle_other9.176
r_dihedral_angle_1_deg8.435
r_scbond_it6.647
r_scbond_other6.596
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.585
r_dihedral_angle_3_deg17.989
r_long_range_B_refined12.295
r_long_range_B_other12.292
r_scangle_other9.552
r_mcangle_it9.177
r_mcangle_other9.176
r_dihedral_angle_1_deg8.435
r_scbond_it6.647
r_scbond_other6.596
r_mcbond_it6.505
r_mcbond_other6.503
r_angle_refined_deg1.497
r_angle_other_deg0.475
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4113
Nucleic Acid Atoms
Solvent Atoms14
Heterogen Atoms98

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing