4ABZ | pdb_00004abz

TetR(D) in Complex with Tigecycline and Magnesium, co-crystallized

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XPV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	291	Protein: 10.0 mg/mL TetR(D), 0.2M NaCl, 50 mM Tris/HCl, pH 8.0, 2mM [TigeTC], 2mM MgCl2. Precipitant: 1M (NH4)2SO4, 0.2M NaCl, 0.05M Tris/HCl, pH 8.0, 10mM MgCl2. Protein/precipitant 2+2 microL, against 0.5mL Precipitant.

Crystal Properties
Matthews coefficient	Solvent content
2.77	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.49	α = 90
b = 68.49	β = 90
c = 179.25	γ = 90

Symmetry
Space Group	I 41 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	MARMOSAIC 225 mm CCD		2011-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.950000	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.85	50	98.2	0.05	0.05	33.95	14.15		18428			41

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.9	97.2		1.9	2.04	14.19

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	2xpv	1.886	48.477	17367	880	98.219	0.215	0.2131	0.22	0.2583	0.26	37.603

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]
1.335			1.335		-2.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.08
r_dihedral_angle_4_deg	22.541
r_dihedral_angle_3_deg	16.243
r_dihedral_angle_1_deg	6.634
r_lrange_it	5.631
r_lrange_other	5.631
r_scangle_it	4.03
r_scangle_other	4.03
r_mcangle_it	3.27
r_mcangle_other	3.269
r_scbond_it	2.587
r_scbond_other	2.585
r_mcbond_it	2.22
r_mcbond_other	2.217
r_angle_refined_deg	1.982
r_angle_other_deg	1.539
r_nbd_other	0.242
r_nbd_refined	0.237
r_symmetry_xyhbond_nbd_refined	0.228
r_symmetry_nbd_other	0.2
r_symmetry_nbd_refined	0.193
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.129
r_symmetry_nbtor_other	0.093
r_chiral_restr	0.089
r_xyhbond_nbd_other	0.07
r_bond_refined_d	0.014
r_metal_ion_refined	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1550
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	46

Software

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