4TXV | pdb_00004txv

Crystal structure of the mixed disulfide intermediate between thioredoxin-like TlpAs(C110S) and subunit II of cytochrome c oxidase CoxBPD (C233S)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JFU	PDB entriues 1JFU and 1m56
experimental model	PDB	1M56	PDB entriues 1JFU and 1m56

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	292	20% PEG2000 MME, 0.8M formic acid/NaOH, 0.1 M Na-cacodylate

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.83	α = 90
b = 81.64	β = 90
c = 109.37	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77	PIXEL	DECTRIS PILATUS 6M		2013-11-22	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)	Rrim 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	50	98.8	0.063	0.074	13.57	3.48		45680		-3	40.055

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05	96.6		0.817	0.963	1.62

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	PDB entriues 1JFU and 1m56	2	65.42	45680	2304	99.11	0.1654	0.1629	0.17	0.2116	0.21	RANDOM	39.402

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]
-1.2			-0.65		1.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.669
r_dihedral_angle_4_deg	22.377
r_dihedral_angle_3_deg	16.154
r_dihedral_angle_1_deg	6.759
r_mcangle_it	4.317
r_mcbond_it	3.146
r_mcbond_other	3.145
r_angle_refined_deg	1.825
r_angle_other_deg	0.882
r_chiral_restr	0.115

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.669
r_dihedral_angle_4_deg	22.377
r_dihedral_angle_3_deg	16.154
r_dihedral_angle_1_deg	6.759
r_mcangle_it	4.317
r_mcbond_it	3.146
r_mcbond_other	3.145
r_angle_refined_deg	1.825
r_angle_other_deg	0.882
r_chiral_restr	0.115
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4823
Nucleic Acid Atoms
Solvent Atoms	444
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
REFMAC	refinement
XDS	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.