Experiment: 3VL3

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	PEG 3350, calcium chloride, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.824	α = 90
b = 57.877	β = 119.02
c = 75.671	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	293	CCD	ADSC QUANTUM 210r		2010-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	0.700	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	1.8	50	91.6	0.06	15.7	2.9		33575

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	1.8	1.83	95.6		0.328		2.8	1697

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3VKZ	1.8	33.09	33560	1680	91.26	0.1592	0.157	0.202	RANDOM	19.2431

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]
0.11		0.06	0.28		-0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.643
r_dihedral_angle_4_deg	19.362
r_dihedral_angle_3_deg	15.944
r_scangle_it	6.842
r_dihedral_angle_1_deg	6.089
r_scbond_it	4.219
r_mcangle_it	2.748
r_angle_refined_deg	2.401
r_mcbond_it	1.642
r_chiral_restr	0.195

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.643
r_dihedral_angle_4_deg	19.362
r_dihedral_angle_3_deg	15.944
r_scangle_it	6.842
r_dihedral_angle_1_deg	6.089
r_scbond_it	4.219
r_mcangle_it	2.748
r_angle_refined_deg	2.401
r_mcbond_it	1.642
r_chiral_restr	0.195
r_bond_refined_d	0.03
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2759
Nucleic Acid Atoms
Solvent Atoms	275
Heterogen Atoms	14

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

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.