7OMX | pdb_00007omx

Thermus sp. 2.9 DarT in complex with carba-NAD+

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7OMV	D_1292116023

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	64 mM potassium thiocyanate, 20% (w/v) PEG2000MME

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.034	α = 90
b = 71.282	β = 90
c = 85.542	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		2019-08-04	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	1.52	54.77	99.3	0.1	0.109	0.043	0.997	8.8	6		33587

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	1.52	1.56			0.932	1.072	0.514	0.581	1.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	D_1292116023	1.52	42.771	33520	1642	99.139	0.175	0.1733	0.18	0.2027	0.21	18.143

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]
-1.115			1.053		0.062

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.206
r_dihedral_angle_4_deg	15.148
r_dihedral_angle_3_deg	12.444
r_dihedral_angle_1_deg	6.775
r_lrange_it	4.43
r_lrange_other	4.242
r_scangle_it	2.195
r_scangle_other	2.171
r_angle_refined_deg	1.53
r_scbond_it	1.433
r_mcangle_it	1.418
r_mcangle_other	1.418
r_scbond_other	1.379
r_angle_other_deg	1.356
r_mcbond_it	0.874
r_mcbond_other	0.872
r_symmetry_xyhbond_nbd_refined	0.218
r_nbd_other	0.215
r_symmetry_nbd_refined	0.214
r_nbd_refined	0.195
r_nbtor_refined	0.181
r_symmetry_nbd_other	0.177
r_xyhbond_nbd_other	0.166
r_xyhbond_nbd_refined	0.14
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.081
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1607
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms	47

Software

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