7DE8 | pdb_00007de8

Crystal Structure of outer membrane protein PorB with G103K mutations from Neisseria meningitidis W135

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3VY8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	100 mM MES, pH 6.5 31% Jeffamine M-600

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.396	α = 90
b = 84.396	β = 90
c = 107.11	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	100	PIXEL	DECTRIS PILATUS3 6M		2014-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1	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	2.75	43.3	99.8	0.077	22.6	6.7		11223

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	2.75	2.81			0.84

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3VY8	2.76	43.237	11178	564	99.795	0.216	0.2132	0.22	0.2603	0.26	90.754

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]
3.893	1.946		3.893		-12.628

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.718
r_dihedral_angle_3_deg	17.112
r_lrange_it	13.475
r_lrange_other	13.473
r_dihedral_angle_4_deg	11.81
r_scangle_it	10.191
r_scangle_other	10.191
r_mcangle_it	8.916
r_mcangle_other	8.915
r_dihedral_angle_1_deg	7.77
r_scbond_it	6.696
r_scbond_other	6.696
r_mcbond_it	6.182
r_mcbond_other	6.179
r_angle_other_deg	1.509
r_angle_refined_deg	1.466
r_nbd_other	0.254
r_symmetry_nbd_refined	0.239
r_symmetry_nbd_other	0.213
r_nbd_refined	0.191
r_symmetry_xyhbond_nbd_refined	0.183
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.152
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.067
r_symmetry_xyhbond_nbd_other	0.062
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2598
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
REFMAC	phasing