6DXN | pdb_00006dxn

1.95 Angstrom Resolution Crystal Structure of DsbA Disulfide Interchange Protein from Klebsiella pneumoniae.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4OCF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	292	Protein: 9.6mg/ml, 0.01M Tris-HCl pH 8.3; Screen: PEGs II (B9), 0.1M Tris-HCl pH 8.5, 30% (v/v) PEG 400.

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.401	α = 90.27
b = 42.392	β = 89.78
c = 103.949	γ = 96

Symmetry
Space Group	P 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	CCD	MARMOSAIC 300 mm CCD	C(111)	2018-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	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	1.95	30	97.8	0.135	0.135	0.154	0.073	16.8	4.4		51946		-3	18.5

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)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	1.98	96.3		0.786	0.786	0.897	0.43	0.726	2.7	4.3

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	4OCF	1.95	27.01	48932	2397	96.41	0.18213	0.17973	0.21	0.22982	0.26	RANDOM	22.852

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]
-0.36	12.88	0.65	3.66	-13.9	-3.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.586
r_dihedral_angle_3_deg	9.702
r_dihedral_angle_4_deg	8.881
r_long_range_B_refined	4.329
r_long_range_B_other	4.232
r_dihedral_angle_1_deg	2.712
r_mcangle_it	2.599
r_mcangle_other	2.598
r_scangle_other	2.387
r_mcbond_it	1.671
r_mcbond_other	1.67
r_scbond_it	1.625
r_scbond_other	1.624
r_angle_refined_deg	1.133
r_angle_other_deg	0.427
r_chiral_restr	0.056
r_gen_planes_refined	0.038
r_gen_planes_other	0.034
r_bond_refined_d	0.006
r_bond_other_d	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	6032
Nucleic Acid Atoms
Solvent Atoms	365
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MrBUMP	phasing