8Q2A

TtX122B - A domain of unknown function from the Teredinibacter turnerae protein TERTU_2913

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Structure of TtX122A currently also being deposited

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292	0.2 M NaCl, 25% PEG3350 and 0.1 M Bis-Tris pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
	34.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.141	α = 90
b = 75.324	β = 90
c = 116.863	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 PILATUS3 6M		2018-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96863	Diamond	I24

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	2.2	46.69	99.8	0.365	0.432	0.228	0.601	6.2	6.8		31699

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	2.2	2.27			2.304	2.805	1.568	0.726		5.6

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-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.2	46.69	31624	1583	99.694	0.211	0.2085	0.259	14.89

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]
-1.366			1.98		-0.614

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.57
r_dihedral_angle_3_deg	15.435
r_dihedral_angle_2_deg	8.922
r_dihedral_angle_1_deg	8.816
r_lrange_it	6.288
r_lrange_other	6.276
r_scangle_it	5.058
r_scangle_other	5.057
r_mcangle_it	3.387
r_mcangle_other	3.387
r_scbond_it	3.326
r_scbond_other	3.325
r_mcbond_it	2.249
r_mcbond_other	2.248
r_angle_refined_deg	2.031
r_angle_other_deg	0.723
r_symmetry_xyhbond_nbd_refined	0.213
r_nbd_other	0.211
r_symmetry_nbd_other	0.207
r_nbd_refined	0.203
r_nbtor_refined	0.189
r_xyhbond_nbd_refined	0.186
r_symmetry_nbd_refined	0.179
r_metal_ion_refined	0.148
r_ncsr_local_group_1	0.12
r_ncsr_local_group_2	0.116
r_ncsr_local_group_3	0.11
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.094
r_bond_refined_d	0.016
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5329
Nucleic Acid Atoms
Solvent Atoms	163
Heterogen Atoms	3

Software

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