5Y2E | pdb_00005y2e

Crystal structure of the oligomerization domain of NSP4 from the rotavirus strain NCDV

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	5.6	289	0.1M tri-Sodium citrate dehydrate, 0.5M ammonium sulfate, 1.0M lithium sulfate monohydrate

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.35	α = 90
b = 48.14	β = 90
c = 122.61	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	100	IMAGE PLATE	MAR scanner 345 mm plate		2008-08-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.7	61.38	94.2	0.998	8.8	4		7012

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.7	61.38	6980	336	93.18	0.2389	0.2372	0.24	0.2735	0.28	RANDOM	65.687

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]
4.35			0.89		-5.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.5
r_dihedral_angle_3_deg	21.787
r_dihedral_angle_4_deg	21.372
r_mcangle_it	6.203
r_mcbond_it	4.042
r_mcbond_other	4.039
r_dihedral_angle_1_deg	3.916
r_angle_other_deg	3.633
r_angle_refined_deg	1.728
r_chiral_restr	0.093

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.5
r_dihedral_angle_3_deg	21.787
r_dihedral_angle_4_deg	21.372
r_mcangle_it	6.203
r_mcbond_it	4.042
r_mcbond_other	4.039
r_dihedral_angle_1_deg	3.916
r_angle_other_deg	3.633
r_angle_refined_deg	1.728
r_chiral_restr	0.093
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1395
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
Aimless	data scaling
PHASER	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.