3DZM | pdb_00003dzm

Crystal structure of a major outer membrane protein from Thermus thermophilus HB27

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	291	0.2M sodium malonate, 44% MPD, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
2	VAPOR DIFFUSION, HANGING DROP	9	291	0.2M sodium malonate, 43% MPD, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 166.98	α = 90
b = 166.98	β = 90
c = 98.12	γ = 120

Symmetry
Space Group	P 31 2 1

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	ADSC QUANTUM 315	mirrors	2008-03-01	M	SINGLE WAVELENGTH
2	1	x-ray	100	PIXEL	PSI PILATUS 6M	mirrors	2008-04-09	M	SINGLE WAVELENGTH
3	1	x-ray	100	PIXEL	PSI PILATUS 6M	mirrors	2008-05-05	M	SINGLE WAVELENGTH
1,2,3	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.072	ESRF	ID23-1
2	SYNCHROTRON	SLS BEAMLINE X06SA	0.9252	SLS	X06SA
3	SYNCHROTRON	SLS BEAMLINE X06SA	1.0162	SLS	X06SA

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
1,2,3	2.8	40	99.5	0.097		9.8	38811	38811		-3	86.43

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)
1,2,3	2.8	2.97	97.2		1.034	1.42	10.1	6196

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	SIRAS	2.801	37.126	2	38810	38810	1946	99.53	0.198	0.196	0.1967	0.234	0.2305	5% of reflections, selected randomly	100.676

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]
0.925			0.925		-1.85

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.892
f_angle_d	1.649
f_chiral_restr	0.102
f_bond_d	0.013
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4626
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms	129

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
SHARP	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.