7AHZ | pdb_00007ahz

Crystal structure of Western clawed frog MDM2 RING domain homodimer bound to UbcH5B-Ub


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72920.1 M HEPES, 10 % w/v PEG 20000
Crystal Properties
Matthews coefficientSolvent content
2.5952.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.03α = 90
b = 153.15β = 107.01
c = 82.08γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2017-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

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
11.8252.62398.10.99813.83.4113701
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)
11.821.850.652

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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-VALUE5MNJ1.8252.623113660551698.0250.1970.19490.20.23050.2348.798
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]
-0.827-0.094-3.2373.472
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.461
r_dihedral_angle_4_deg15.583
r_dihedral_angle_3_deg14.674
r_lrange_it9.507
r_lrange_other9.491
r_scangle_it7.754
r_scangle_other7.753
r_dihedral_angle_1_deg6.253
r_mcangle_it5.581
r_mcangle_other5.58
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8781
Nucleic Acid Atoms
Solvent Atoms356
Heterogen Atoms9

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing