Experiment: 3PVN

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LJ7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	289	12% PEG 4000, 0.1M Tris-Hcl, 0.2M MgCl2, 0.05M LiCl, pH 8.0, VAPOR DIFFUSION, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.3	α = 79.9
b = 96.4	β = 77.1
c = 160.4	γ = 69.4

Symmetry
Space Group	P 1

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	MARMOSAIC 225 mm CCD		2008-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87260	ESRF	ID23-2

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	1.98	20	92.8	0.062	9.7	1.94	275048	275047		-3	29.7

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	1.98	2.05	91.7		0.321	2.96	1.85	19869

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	1LJ7	1.98	19.92	-3	261507	261507	13541	100	0.19156	0.17857	0.17564	0.23551	RANDOM	23.649

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]
0.54	-0.34	0.24	-0.16	0.27	-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.541
r_dihedral_angle_4_deg	24.998
r_dihedral_angle_3_deg	16.213
r_dihedral_angle_1_deg	6.843
r_scangle_it	5.249
r_scbond_it	3.448
r_mcangle_it	2.248
r_angle_refined_deg	1.938
r_mcbond_it	1.276
r_chiral_restr	0.168

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.541
r_dihedral_angle_4_deg	24.998
r_dihedral_angle_3_deg	16.213
r_dihedral_angle_1_deg	6.843
r_scangle_it	5.249
r_scbond_it	3.448
r_mcangle_it	2.248
r_angle_refined_deg	1.938
r_mcbond_it	1.276
r_chiral_restr	0.168
r_bond_refined_d	0.024
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	32640
Nucleic Acid Atoms
Solvent Atoms	3011
Heterogen Atoms	45

Software

Software
Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	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.