7EVG | pdb_00007evg

Apo Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a psuedo-protofilament arrangement

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6O2R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	25% PEG 1500, 0.1 M SPG, pH 7.0, soaked with 100 mM phosphate for 2 h

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.102	α = 90
b = 94.184	β = 90
c = 100.755	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		2021-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.48	47.1	99.7	0.185	0.201	0.078	8.6	6.6		14154

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	2.48	2.57			1.23	1.34	0.516	0.576	1.7

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6o2r	2.48	44.4	14104	701	99.8	0.211	0.21	0.257	0.26	49.38

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.1142
f_angle_d	0.5323
f_chiral_restr	0.0426
f_plane_restr	0.0037
f_bond_d	0.0023

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3353
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms	5

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	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.