5C91

NEDD4 HECT with covalently bound indole-based inhibitor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293100 mM MES, 35 mM calcium chloride, 5 mM TCEP, 6% PEG400
Crystal Properties
Matthews coefficientSolvent content
2.2946.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 175.2α = 90
b = 38.73β = 93.13
c = 60.36γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2014-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.033APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.4432.298.20.0910.07111.23.21510523.03
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.442.598.70.6020.47223.11087

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2XBF2.4431.861437173197.830.25010.24780.2977RANDOM50.376
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]
-2.69-1.091.631.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.891
r_dihedral_angle_4_deg16.096
r_dihedral_angle_3_deg15.789
r_dihedral_angle_1_deg4.984
r_mcangle_it2.618
r_mcbond_it1.48
r_mcbond_other1.48
r_angle_refined_deg1.036
r_angle_other_deg0.711
r_chiral_restr0.057
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.891
r_dihedral_angle_4_deg16.096
r_dihedral_angle_3_deg15.789
r_dihedral_angle_1_deg4.984
r_mcangle_it2.618
r_mcbond_it1.48
r_mcbond_other1.48
r_angle_refined_deg1.036
r_angle_other_deg0.711
r_chiral_restr0.057
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3156
Nucleic Acid Atoms
Solvent Atoms7
Heterogen Atoms23

Software

Software
Software NamePurpose
xia2data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction