3E9J | pdb_00003e9j

Structure of the charge-transfer intermediate of the transmembrane redox catalyst DsbB

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HI7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.9	277	23% PEG550 MME, 50 mM Tris pH 8.9, 1.0 M ammonium formate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
5.110001	75.929558

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.305	α = 90
b = 103.105	β = 91.16
c = 125.826	γ = 90

Symmetry
Space Group	P 1 21 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 225 mm CCD		2006-08-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.920	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	3.7	125	98	0.072	9.9	3.1		18142		3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3.7	3.9	99.1		0.436	2	3.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2HI7	3.7	125.99	18142	17000	726	97.22	0.33893	0.33733	0.33	0.37903	0.39	RANDOM	160.416

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]
-23.32		-2.51	20.62		2.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.477
r_dihedral_angle_3_deg	22.549
r_dihedral_angle_4_deg	17.467
r_dihedral_angle_1_deg	8.53
r_angle_refined_deg	1.418
r_angle_other_deg	0.973
r_symmetry_vdw_refined	0.388
r_nbd_refined	0.268
r_nbd_other	0.219
r_xyhbond_nbd_refined	0.206
r_nbtor_refined	0.198
r_symmetry_vdw_other	0.136
r_xyhbond_nbd_other	0.111
r_nbtor_other	0.094
r_chiral_restr	0.074
r_bond_refined_d	0.013
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
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	5112
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
CLARA	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing