5RYP

EPB41L3 PanDDA analysis group deposition -- Crystal Structure of the FERM domain of human EPB41L3 in complex with Z1929757385


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62980.075M ammonium nitrate, 0.1M MES pH 6.0, 6.5% PEG 2000, 6.5% PEG 3350, 6.5% PEG 4000, 6.5% PEG 5000, 10% ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.2244.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.58α = 90
b = 77.01β = 90
c = 99.88γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-07-12SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

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
11.6341.999.90.0840.0920.0360.99811.16.238029
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)
11.631.671001.2571.3980.60.5215.32788

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT6IBE1.6341.9436065189899.860.21490.21320.2473RANDOM30.659
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]
-0.210.9-0.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.012
r_dihedral_angle_4_deg18.274
r_dihedral_angle_3_deg16.388
r_dihedral_angle_1_deg7.03
r_mcangle_it3.497
r_mcbond_other2.209
r_mcbond_it2.208
r_angle_refined_deg1.542
r_angle_other_deg1.331
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.012
r_dihedral_angle_4_deg18.274
r_dihedral_angle_3_deg16.388
r_dihedral_angle_1_deg7.03
r_mcangle_it3.497
r_mcbond_other2.209
r_mcbond_it2.208
r_angle_refined_deg1.542
r_angle_other_deg1.331
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2335
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing