5RYU | pdb_00005ryu

EPB41L3 PanDDA analysis group deposition -- Crystal Structure of the FERM domain of human EPB41L3 in complex with Z1545196403

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	0.075M 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 coefficient	Solvent content
2.21	44.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.445	α = 90
b = 77.283	β = 90
c = 99.439	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2019-07-12		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.63	77.29	100	0.089	0.097	0.039	0.998	9.8	6.2		37872

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)	Redundancy	Number Unique Reflections (All)
1	1.63	1.67	99.8		1.364	1.525	0.67	0.486		5.1	2760

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (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 Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	6IBE	1.63	61.02	35907	1890	99.88	0.2106	0.2087	0.23	0.2472	0.26	RANDOM	28.917

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]
-0.39			1.72		-1.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.497
r_dihedral_angle_4_deg	17.36
r_dihedral_angle_3_deg	15.961
r_dihedral_angle_1_deg	7.014
r_mcangle_it	2.989
r_mcbond_other	1.785
r_mcbond_it	1.781
r_angle_refined_deg	1.478
r_angle_other_deg	1.301
r_chiral_restr	0.072

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.497
r_dihedral_angle_4_deg	17.36
r_dihedral_angle_3_deg	15.961
r_dihedral_angle_1_deg	7.014
r_mcangle_it	2.989
r_mcbond_other	1.785
r_mcbond_it	1.781
r_angle_refined_deg	1.478
r_angle_other_deg	1.301
r_chiral_restr	0.072
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2335
Nucleic Acid Atoms
Solvent Atoms	150
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.