Experiment: 3VNY

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	2.0M sodium phosphate monobasic monohydrate/potassium phosphate dibasic (0.5/9.5 [v/v]), VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.126	α = 90
b = 101.126	β = 90
c = 217.881	γ = 90

Symmetry
Space Group	I 41 2 2

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 270		2010-01-29	M	SINGLE WAVELENGTH
2	1	x-ray	95	CCD	ADSC QUANTUM 270		2010-01-29	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.0000	Photon Factory	AR-NE3A
2	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	0.97946, 0.97967, 0.96000	Photon Factory	AR-NE3A

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	1.5	30.684	100	0.062	47	14.6		90146			14.5

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	1.5	1.53	100		0.392	6.8	14.4	4427

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.5	30.58	85363	4504	99.71	0.17264	0.17173	0.18987	RANDOM	15.946

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]
0.05			0.05		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.544
r_dihedral_angle_4_deg	16.807
r_dihedral_angle_3_deg	12.771
r_dihedral_angle_1_deg	5.576
r_scangle_it	2.295
r_scbond_it	1.411
r_angle_refined_deg	1.066
r_mcangle_it	0.905
r_mcbond_it	0.481
r_chiral_restr	0.073

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.544
r_dihedral_angle_4_deg	16.807
r_dihedral_angle_3_deg	12.771
r_dihedral_angle_1_deg	5.576
r_scangle_it	2.295
r_scbond_it	1.411
r_angle_refined_deg	1.066
r_mcangle_it	0.905
r_mcbond_it	0.481
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3531
Nucleic Acid Atoms
Solvent Atoms	503
Heterogen Atoms	17

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.