2NS7 | pdb_00002ns7

How an in vitro selected peptide mimics the antibiotic tetracycline to induce TET repressor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NS8	2NS8 (Chain A+B)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	292	1.4M ammonium sulfate, 0.1M sodium chloride, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.91	α = 90
b = 107.91	β = 90
c = 303.94	γ = 120

Symmetry
Space Group	P 61 2 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	CCD	MAR CCD 165 mm	mirrors	2004-12-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.946452	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.4	37.04	98.4	0.061	28.43			41266		-3	59.819

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.45	98		0.472	4.9		2396

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2NS8 (Chain A+B)	2.4	37.04	41265	3302	100	0.234	0.23	0.24	0.277	0.28	RANDOM	61.794

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]
3.34	1.67		3.34		-5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.995
r_dihedral_angle_3_deg	17.937
r_dihedral_angle_4_deg	15.449
r_dihedral_angle_1_deg	5.614
r_scangle_it	1.615
r_angle_refined_deg	1.202
r_scbond_it	1.079
r_angle_other_deg	0.805
r_mcangle_it	0.748
r_mcbond_it	0.641
r_symmetry_vdw_other	0.229
r_nbd_refined	0.206
r_symmetry_vdw_refined	0.201
r_nbtor_refined	0.172
r_nbd_other	0.158
r_xyhbond_nbd_refined	0.15
r_symmetry_hbond_refined	0.13
r_nbtor_other	0.086
r_mcbond_other	0.082
r_chiral_restr	0.065
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6027
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
AMoRE	phasing