Experiment: 2P3I

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KQR	RRV VP8* structure PDB code 1KQR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	303	1.7M (NH4)2SO4, 2.4% v/v PEG 400, 0.1M PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.549	α = 90
b = 48.549	β = 90
c = 131.639	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	295	CCD	BRUKER SMART 6000	mirrors	2004-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	MACSCIENCE	1.5418

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	1.75	48.54	99.7	0.063	8.8	19.9	16731	16731

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)
	1.75	1.83	100		0.3	1.9		2100

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	RRV VP8* structure PDB code 1KQR	1.75	20	15805	842	99.98	0.16388	0.16262	0.16	0.18773	0.19	RANDOM	14.988

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]
0.06			0.06		-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.201
r_dihedral_angle_3_deg	12.296
r_dihedral_angle_4_deg	8.704
r_dihedral_angle_1_deg	6.145
r_scangle_it	3.056
r_scbond_it	2.071
r_angle_refined_deg	1.304
r_mcangle_it	1.253
r_mcbond_it	0.788
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.201
r_dihedral_angle_3_deg	12.296
r_dihedral_angle_4_deg	8.704
r_dihedral_angle_1_deg	6.145
r_scangle_it	3.056
r_scbond_it	2.071
r_angle_refined_deg	1.304
r_mcangle_it	1.253
r_mcbond_it	0.788
r_nbtor_refined	0.307
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.147
r_xyhbond_nbd_refined	0.132
r_symmetry_hbond_refined	0.111
r_chiral_restr	0.09
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1280
Nucleic Acid Atoms
Solvent Atoms	133
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data collection
SAINT	data reduction
LSCALE	data scaling
AMoRE	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 R01GM157729.