Experiment: 2DUP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP, SOAKING	6.5	277	Crystallization: 15% PEG4000, 1.5M NaCl, 0.1M MES (pH6.5), 10mM EDTA, VAPOR DIFFUSION, HANGING DROP, SOAKING, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 171	α = 90
b = 45.2	β = 132.6
c = 117.1	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	ADSC QUANTUM 210		2005-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.1	50	93.7	0.083	13.4	3.5	38945	36474			34

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18	78.9		0.314	3.7	3.4	3041

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 2DUO	2.1	20	34622	34622	1828	93.7	0.228	0.228	0.225	0.278	RANDOM	39.27

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]
2.81		3.4	-0.29		2.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.862
r_dihedral_angle_3_deg	15.913
r_dihedral_angle_4_deg	15.569
r_dihedral_angle_1_deg	6.57
r_scangle_it	2.571
r_scbond_it	1.74
r_mcangle_it	1.503
r_angle_refined_deg	1.336
r_mcbond_it	0.912
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.862
r_dihedral_angle_3_deg	15.913
r_dihedral_angle_4_deg	15.569
r_dihedral_angle_1_deg	6.57
r_scangle_it	2.571
r_scbond_it	1.74
r_mcangle_it	1.503
r_angle_refined_deg	1.336
r_mcbond_it	0.912
r_nbtor_refined	0.308
r_symmetry_hbond_refined	0.204
r_symmetry_vdw_refined	0.203
r_nbd_refined	0.193
r_xyhbond_nbd_refined	0.155
r_metal_ion_refined	0.143
r_chiral_restr	0.092
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3913
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms	23

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

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 R01GM133198.