5RZX

EPB41L3 PanDDA analysis group deposition -- Crystal Structure of the FERM domain of human EPB41L3 in complex with Z2856434814


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
2.2144.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.29α = 90
b = 76.78β = 90
c = 100.23γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-08-02SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91589DiamondI04-1

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
11.7450.1299.50.0870.0950.0370.99811.36.530995
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)
11.741.7999.91.6671.830.7420.45562238

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 SYNTHESISTHROUGHOUT6IBE1.7450.1729375156699.390.22020.21810.2613RANDOM36.225
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]
-1.061.53-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.883
r_dihedral_angle_3_deg16.452
r_dihedral_angle_4_deg15.686
r_dihedral_angle_1_deg7.113
r_mcangle_it3.971
r_mcbond_other2.394
r_mcbond_it2.392
r_angle_refined_deg1.469
r_angle_other_deg1.285
r_chiral_restr0.067
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.883
r_dihedral_angle_3_deg16.452
r_dihedral_angle_4_deg15.686
r_dihedral_angle_1_deg7.113
r_mcangle_it3.971
r_mcbond_other2.394
r_mcbond_it2.392
r_angle_refined_deg1.469
r_angle_other_deg1.285
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2335
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing