7OMU | pdb_00007omu

Thermosipho africanus DarTG in complex with ADP-ribose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5M31

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	0.2 M potassium thiocyanate, 0.1 M TRIS pH 7.5, 8% (w/v) PEG 20,000, 8% (v/v) PEG500MME

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 187.458	α = 90
b = 187.458	β = 90
c = 187.458	γ = 90

Symmetry
Space Group	I 2 3

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-F		2016-09-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	2.96	93.73	100	0.074	0.078	0.024	1	17.3	10.7		22975

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	2.96	3.04			1.713	1.799	0.545	0.533	1.5

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	5M31	2.96	76.647	22813	1142	99.455	0.213	0.2107	0.21	0.2482	0.24	102.859

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
r_dihedral_angle_2_deg	31.398
r_dihedral_angle_3_deg	16.951
r_dihedral_angle_4_deg	16.171
r_lrange_it	7.806
r_lrange_other	7.805
r_dihedral_angle_1_deg	6.652
r_mcangle_it	4.684
r_mcangle_other	4.684
r_scangle_it	4.337
r_scangle_other	4.337
r_mcbond_it	2.698
r_mcbond_other	2.696
r_scbond_it	2.447
r_scbond_other	2.447
r_angle_refined_deg	1.244
r_angle_other_deg	1.053
r_symmetry_xyhbond_nbd_refined	0.269
r_nbd_refined	0.179
r_nbd_other	0.179
r_symmetry_nbd_other	0.17
r_nbtor_refined	0.158
r_symmetry_nbd_refined	0.139
r_xyhbond_nbd_refined	0.099
r_symmetry_nbtor_other	0.074
r_ncsr_local_group_1	0.06
r_chiral_restr	0.046
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6122
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	72

Software

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