5J9H | pdb_00005j9h

Crystal structure of Glycoprotein C from Puumala virus in the post-fusion conformation (pH 8.0)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5J81

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	289	40% PEG 400 0.2 M Lithium sulphate 0.1 M Tris buffer pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.521	α = 90
b = 138.521	β = 90
c = 138.521	γ = 90

Symmetry
Space Group	I 21 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2015-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97949	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.5	49	99.6	0.072	0.998	14.43	5.5		15391		-3	60.944

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	2.5	2.53	99.6		0.783	2.15

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	MOLECULAR REPLACEMENT	THROUGHOUT	5J81	2.5	49	14611	780	99.55	0.211	0.2085	0.22	0.2579	0.22	RANDOM	67.716

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.944
r_dihedral_angle_3_deg	14.355
r_dihedral_angle_4_deg	10.663
r_dihedral_angle_1_deg	7.386
r_mcangle_it	1.492
r_angle_refined_deg	1.271
r_angle_other_deg	0.856
r_mcbond_it	0.83
r_mcbond_other	0.83
r_chiral_restr	0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.944
r_dihedral_angle_3_deg	14.355
r_dihedral_angle_4_deg	10.663
r_dihedral_angle_1_deg	7.386
r_mcangle_it	1.492
r_angle_refined_deg	1.271
r_angle_other_deg	0.856
r_mcbond_it	0.83
r_mcbond_other	0.83
r_chiral_restr	0.07
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3149
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms	44

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	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.