7OMV

Thermus sp. 2.9 DarT

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7OMU	D_1292116031

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	100 mM potassium thiocyanate, 30% (w/v) PEG2000MME

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.317	α = 90
b = 90.77	β = 90
c = 34.948	γ = 90

Symmetry
Space Group	P 21 21 2

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		2019-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.29	90.77	96.9	0.079	0.082	0.023	0.998	15	11.3		48391

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	1.29	1.31			0.368	0.406	0.166	0.934	2.9

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	D_1292116031	1.29	45.426	48332	2439	96.658	0.163	0.1614	0.2022	19.362

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]
-3.487			0.047		3.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.804
r_dihedral_angle_4_deg	15.658
r_rigid_bond_restr	12.695
r_dihedral_angle_3_deg	12.676
r_lrange_it	8.611
r_dihedral_angle_1_deg	6.639
r_lrange_other	6.329
r_scangle_other	4.632
r_scangle_it	4.603
r_scbond_other	3.718
r_scbond_it	3.645
r_mcangle_it	2.657
r_mcangle_other	2.656
r_mcbond_other	2.324
r_mcbond_it	2.321
r_angle_refined_deg	1.792
r_angle_other_deg	1.432
r_symmetry_xyhbond_nbd_refined	0.237
r_nbd_refined	0.205
r_symmetry_nbd_other	0.181
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.157
r_symmetry_nbd_refined	0.138
r_nbd_other	0.13
r_chiral_restr	0.101
r_symmetry_nbtor_other	0.082
r_xyhbond_nbd_other	0.016
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1730
Nucleic Acid Atoms
Solvent Atoms	219
Heterogen Atoms	4

Software

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