6EHC

OmpUdeltaN (N-terminus deletion mutant of OmpU), outer membrane protein of Vibrio cholerae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6EHB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	298	33% PEG 300, 0.1 M NaCl, 0.05 M bicine

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.36	α = 90
b = 81.36	β = 90
c = 198.5	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	PIXEL	DECTRIS PILATUS 6M-F		2017-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.920	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.02	57.52	100	0.9	12.3	11.5		48646

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.02		100		0.6	1.3	11.4

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6EHB	2.02	57.52	46172	2419	99.97	0.19533	0.1926	0.24761	RANDOM	39.774

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]
-1.74	-0.87		-1.74		5.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.655
r_dihedral_angle_4_deg	16.4
r_dihedral_angle_3_deg	14.124
r_long_range_B_refined	7.164
r_long_range_B_other	7.164
r_dihedral_angle_1_deg	6.967
r_scangle_other	5.392
r_mcangle_it	4.209
r_mcangle_other	4.209
r_scbond_it	3.636
r_scbond_other	3.636
r_mcbond_it	3.011
r_mcbond_other	3.009
r_angle_refined_deg	1.652
r_angle_other_deg	0.943
r_chiral_restr	0.109
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4714
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms	97

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing