Experiment: 2H6Y

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	COUNTER-DIFFUSION	3.5	277	60% (v/v) MPD, AcNa 15 mM pH 3.5, 1 mM Ac2Cu, Counter-diffusion, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.608	α = 90
b = 101.608	β = 90
c = 38.658	γ = 120

Symmetry
Space Group	P 61

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	BRUKER SMART 6000	Montel Optics	2005-12-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	OTHER	1.5418

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	2.4	50.8	99.5	0.048	18.96	10.25	9093	9093			35.742

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)
1	2.4	2.45	93.4		0.3529	3.45	2.9	492

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 (All)	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	2TRX_A	2.4	50.8	9093	8566	408	93.915	0.188	0.188	0.1864	0.18	0.2295	0.22	RANDOM	23.717

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]
-1.442	-0.721		-1.442		2.163

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.261
r_dihedral_angle_4_deg	17.32
r_dihedral_angle_3_deg	15.116
r_dihedral_angle_1_deg	5.665
r_scangle_it	1.478
r_angle_refined_deg	1.228
r_scbond_it	0.897
r_mcangle_it	0.665
r_mcbond_it	0.369
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.261
r_dihedral_angle_4_deg	17.32
r_dihedral_angle_3_deg	15.116
r_dihedral_angle_1_deg	5.665
r_scangle_it	1.478
r_angle_refined_deg	1.228
r_scbond_it	0.897
r_mcangle_it	0.665
r_mcbond_it	0.369
r_nbtor_refined	0.3
r_symmetry_vdw_refined	0.226
r_nbd_refined	0.195
r_symmetry_hbond_refined	0.172
r_xyhbond_nbd_refined	0.119
r_chiral_restr	0.072
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1622
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms	16

Software

Software
Software Name	Purpose
SAINT	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data reduction
SADABS	data scaling
XPREP	data reduction
Coot	model building
MolProbity	model building

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.