5MDS

Crystal structure of outer membrane expressed Chitoporin VhChip from Vibrio harveyi in complex with chitotetraose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5MDO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	28% (w/v) PEG 400, 0.2 M sodium acetate, 0.1 M MES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
4.31	71.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 250.01	α = 90
b = 145.047	β = 94.8
c = 55.158	γ = 90

Symmetry
Space Group	C 1 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	PIXEL	DECTRIS PILATUS 6M		2015-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.979490	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.6	125.35	93.4	0.09	0.081	8.4	2.9		56059

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.68	95.1		0.777	0.699	1.1	2.9

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	5MDO	2.6	125.35	54404	1652	93.15	0.22201	0.22126	0.24749	RANDOM	62.644

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]
2.3		-1.36	-0.79		-1.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.634
r_dihedral_angle_4_deg	17.162
r_dihedral_angle_3_deg	15.183
r_dihedral_angle_1_deg	7.721
r_long_range_B_other	3.825
r_long_range_B_refined	3.823
r_scangle_other	2.699
r_angle_refined_deg	2.085
r_scbond_other	1.752
r_scbond_it	1.751
r_mcangle_it	1.578
r_mcangle_other	1.578
r_angle_other_deg	1.038
r_mcbond_it	0.962
r_mcbond_other	0.962
r_chiral_restr	0.109
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
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	7995
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	171

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing