6XTJ

The high resolution structure of the FERM domain of human FERMT2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5XPY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	0.1M HEPES pH 7.0, 1.4M sodium citrate tribasic

Crystal Properties
Matthews coefficient	Solvent content
3.45	64.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.172	α = 90
b = 145.172	β = 90
c = 59.633	γ = 120

Symmetry
Space Group	P 32 2 1

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 PILATUS3 6M		2019-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	1.6	72.7	100	0.277	0.28	0.071	0.999	11	31.1		95151

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	1.6	1.63	99.7		5.732	5.965	1.638	0.732	1	25.4

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5XPY	1.6	72.7	94810	1874	99.707	0.181	0.1807	0.2037	29.736

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]
0.782	0.391		0.782		-2.536

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.234
r_dihedral_angle_4_deg	21.29
r_dihedral_angle_3_deg	14.463
r_dihedral_angle_1_deg	8.322
r_lrange_it	7.299
r_lrange_other	7.246
r_scangle_it	4.947
r_scangle_other	4.946
r_mcangle_it	3.834
r_mcangle_other	3.833
r_scbond_it	3.044
r_scbond_other	3.026
r_mcbond_other	2.377
r_mcbond_it	2.376
r_angle_other_deg	2.286
r_angle_refined_deg	1.428
r_symmetry_xyhbond_nbd_other	0.459
r_nbd_refined	0.27
r_symmetry_nbd_refined	0.256
r_nbd_other	0.253
r_symmetry_nbd_other	0.224
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.167
r_symmetry_xyhbond_nbd_refined	0.141
r_chiral_restr	0.074
r_symmetry_nbtor_other	0.066
r_bond_other_d	0.034
r_gen_planes_other	0.01
r_gen_planes_refined	0.009
r_bond_refined_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3694
Nucleic Acid Atoms
Solvent Atoms	377
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing