Experiment: 3VYG

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DD5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	293	0.1M potassium phosphate pH 6.8, 1.4M potassium phosphate tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.5	64.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.448	α = 90
b = 172.398	β = 90
c = 172.531	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	95	CCD	ADSC QUANTUM 210r		2011-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.000	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	1.72	50	96.5	0.062			343322	325674

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	1.72	1.78	99.8		0.256	9.2

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	2DD5	1.72	33.96	343322	325672	17284	96.45	0.18899	0.18746	0.19	0.21771	0.22	RANDOM	20.084

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.455
r_dihedral_angle_4_deg	19.931
r_dihedral_angle_3_deg	13.058
r_dihedral_angle_1_deg	11.246
r_scangle_it	4.833
r_scbond_it	3.245
r_angle_refined_deg	2.311
r_mcangle_it	2.215
r_mcbond_it	1.453
r_chiral_restr	0.187

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.455
r_dihedral_angle_4_deg	19.931
r_dihedral_angle_3_deg	13.058
r_dihedral_angle_1_deg	11.246
r_scangle_it	4.833
r_scbond_it	3.245
r_angle_refined_deg	2.311
r_mcangle_it	2.215
r_mcbond_it	1.453
r_chiral_restr	0.187
r_bond_refined_d	0.03
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15702
Nucleic Acid Atoms
Solvent Atoms	1500
Heterogen Atoms	44

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.