Experiment: 2H6X

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	COUNTER-DIFFUSION	3.5	277	60% (v/v) MPD, Ac2Cu 1mM, AcNa 15mM, HEPES 15 mM pH 6.9, pH 3.5, Counterdiffusion, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.727	α = 90
b = 102.727	β = 90
c = 42.865	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	2006-03-28	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	2.6	51.36	99.8	0.0787	9.08	7.28	8147	8147			51.288

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	2.6	2.65	100		0.3161	2.63	7.28	464

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2TRX	2.6	44.5	8147	8077	370	99.18	0.222	0.222	0.219	0.284	RANDOM	43.014

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]
-0.48	-0.24		-0.48		0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.224
r_dihedral_angle_3_deg	16.628
r_dihedral_angle_4_deg	15.798
r_dihedral_angle_1_deg	6.349
r_mcangle_it	1.954
r_scangle_it	1.636
r_angle_refined_deg	1.427
r_mcbond_it	1.193
r_scbond_it	1.142
r_symmetry_hbond_refined	0.366

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.224
r_dihedral_angle_3_deg	16.628
r_dihedral_angle_4_deg	15.798
r_dihedral_angle_1_deg	6.349
r_mcangle_it	1.954
r_scangle_it	1.636
r_angle_refined_deg	1.427
r_mcbond_it	1.193
r_scbond_it	1.142
r_symmetry_hbond_refined	0.366
r_nbtor_refined	0.309
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.21
r_symmetry_vdw_refined	0.181
r_chiral_restr	0.083
r_bond_refined_d	0.014
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1636
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data reduction
SAINT	data scaling
SADABS	data scaling
XPREP	data reduction
AMoRE	phasing
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.