6EHF

OmpT (in-vitro folded), an outer membrane protein Vibrio cholerae (trimer form)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.2	298	0.05 M calcium chloride dihydrate, 0.05 M barium chloride, 0.1 M tris, 32% PEG 400

Crystal Properties
Matthews coefficient	Solvent content
4.45	72.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 200.91	α = 90
b = 200.91	β = 90
c = 200.91	γ = 90

Symmetry
Space Group	I 4 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	298	PIXEL	DECTRIS PILATUS 6M-F		2016-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9762	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	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	2.72	71.03	99	0.025	1	22.1	42.2		18714

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.72		98		0.679	0.6	1.2	43.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6EHD	2.72	71.03	17747	956	98.98	0.24015	0.23798	0.24	0.28059	0.29	RANDOM	96.065

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.924
r_dihedral_angle_4_deg	26.628
r_dihedral_angle_3_deg	17.646
r_long_range_B_refined	13.903
r_long_range_B_other	13.901
r_scangle_other	11.67
r_mcangle_it	10.552
r_mcangle_other	10.549
r_dihedral_angle_1_deg	9.045
r_scbond_it	8.333
r_scbond_other	8.333
r_mcbond_it	7.629
r_mcbond_other	7.629
r_angle_refined_deg	1.91
r_angle_other_deg	1.036
r_chiral_restr	0.109
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
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	2451
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	1

Software

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