6YR2 | pdb_00006yr2

TetR(D) soaked with Tigecycline P4(1)2(1)2

X-RAY DIFFRACTION

---

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	7	291	Native crystal soaked in 1M (NH4)2SO4, 0.2M NaCl, 0.05M Tris/HCl, pH 7.0, 0.142 mM TigeTC, 2mM MgCl2, 14hours.

Crystal Properties
Matthews coefficient	Solvent content
2.24	44.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.339	α = 90
b = 68.339	β = 90
c = 178.397	γ = 90

Symmetry
Space Group	P 41 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	CCD	RIGAKU SATURN 70		2009-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	1.95	42.5	97.9	0.143	7.1	7.33		31779			29

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	1.95	2.02	92.4		0.639	1.4	4.52

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	1.95	37.53	31150	1569	98.076	0.212	0.2102	0.22	0.2374	0.24	34.691

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]
0.435			0.435		-0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.966
r_dihedral_angle_4_deg	16.416
r_dihedral_angle_3_deg	15.895
r_dihedral_angle_1_deg	6.549
r_lrange_it	5.199
r_lrange_other	5.181
r_scangle_it	3.273
r_scangle_other	3.217
r_mcangle_it	2.715
r_mcangle_other	2.715
r_scbond_it	2.02
r_angle_refined_deg	1.964
r_scbond_other	1.95
r_mcbond_it	1.637
r_mcbond_other	1.637
r_angle_other_deg	1.538
r_symmetry_nbd_refined	0.259
r_nbd_refined	0.23
r_nbd_other	0.205
r_symmetry_nbd_other	0.19
r_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.175
r_ncsr_local_group_1	0.147
r_symmetry_xyhbond_nbd_refined	0.137
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.091
r_symmetry_xyhbond_nbd_other	0.043
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3196
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	61

Software

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