3POU | pdb_00003pou

Crystal structure of E.coli OmpF porin in lipidic cubic phase: space group H32, large unit cell

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.6	296	0.1M sodium citrate, 0.7M sodium tartrate, 1.0M potassium thiocyanate, pH 5.6, lipidic sponge phase, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.71	α = 90
b = 85.71	β = 90
c = 332.941	γ = 120

Symmetry
Space Group	H 3 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	mirrors	2008-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00	SLS	X06DA

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	2.8	19.99	99.7	0.329	6.8	9	12017	12017			52.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.95	100		0.014	1.441	1.524	0.492	0.5	9.5	1724

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	2OMF	2.8	19.99	12005	12005	573	99.9	0.1982	0.1955	0.2	0.2515	0.26	RANDOM	48.0181

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]
-0.17	-0.09		-0.17		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.076
r_dihedral_angle_3_deg	17.266
r_dihedral_angle_4_deg	15.837
r_dihedral_angle_1_deg	6.937
r_scangle_it	3.015
r_scbond_it	1.83
r_angle_refined_deg	1.646
r_mcangle_it	1.248
r_mcbond_it	0.651
r_chiral_restr	0.103

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.076
r_dihedral_angle_3_deg	17.266
r_dihedral_angle_4_deg	15.837
r_dihedral_angle_1_deg	6.937
r_scangle_it	3.015
r_scbond_it	1.83
r_angle_refined_deg	1.646
r_mcangle_it	1.248
r_mcbond_it	0.651
r_chiral_restr	0.103
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2627
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	80

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.