3QKX | pdb_00003qkx

Crystal structure of a TetR-family transcriptional regulator (HI0893) from Haemophilus influenzae RD at 2.35 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.33	277	1.80 M lithium sulfate, 0.1M HEPES pH 7.33, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.16	α = 90
b = 71.16	β = 90
c = 159.334	γ = 120

Symmetry
Space Group	P 62

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 325 mm CCD		2010-02-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97954,0.91837,0.97917	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.35	29.56	99.9	0.081	13	7.7	19028	19028			63.528

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.41	99.9		0.013	1.322	1.6	7.7	1392

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.35	29.56	18989	979	99.94	0.224	0.2227	0.22	0.2484	0.24	RANDOM	69.5937

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]
0.14	0.07		0.14		-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.702
r_dihedral_angle_3_deg	16.55
r_dihedral_angle_4_deg	16.512
r_dihedral_angle_1_deg	6.181
r_scangle_it	2.793
r_scbond_it	1.823
r_angle_refined_deg	1.205
r_mcangle_it	1.135
r_angle_other_deg	1.02
r_mcbond_it	0.594

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.702
r_dihedral_angle_3_deg	16.55
r_dihedral_angle_4_deg	16.512
r_dihedral_angle_1_deg	6.181
r_scangle_it	2.793
r_scbond_it	1.823
r_angle_refined_deg	1.205
r_mcangle_it	1.135
r_angle_other_deg	1.02
r_mcbond_it	0.594
r_mcbond_other	0.147
r_chiral_restr	0.062
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2912
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	49

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.