7O6T | pdb_00007o6t

Crystal structure of the polymerising VEL domain of VIN3 (R556D I575D mutant)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.06M Morpheus Divalents, 0.1M Morpheus Buffer System 2 pH 7.5, 10% w/v PEG 8K, 20% v/v ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.423	α = 90
b = 51.809	β = 90
c = 85.01	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 EIGER2 X 16M		2020-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97950	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.02	29.49	99.7	1	36.2	20		9677

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.02	2.07			0.93

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.02	29.49	9131	506	99.71	0.20241	0.21	0.23655	0.26	RANDOM	49.648

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]
-1.23			3.04		-1.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.351
r_dihedral_angle_4_deg	19.995
r_dihedral_angle_3_deg	12.934
r_long_range_B_other	7.851
r_long_range_B_refined	7.845
r_scangle_other	6.328
r_scbond_it	4.05
r_scbond_other	4.049
r_dihedral_angle_1_deg	3.993
r_mcangle_it	3.557
r_mcangle_other	3.555
r_mcbond_other	2.731
r_mcbond_it	2.729
r_angle_refined_deg	1.228
r_angle_other_deg	1.099
r_chiral_restr	0.063
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1173
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
CRANK2	phasing
Coot	model building
PDB_EXTRACT	data extraction