6G43 | pdb_00006g43

Crystal structure of SeMet-labeled mavirus major capsid protein lacking the C-terminal domain

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3.5	293	0.1 M tri-sodium citrate, 1.2 - 1.7 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.59	65.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.35	α = 90
b = 135.3	β = 90
c = 136.04	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	PIXEL	DECTRIS PILATUS 6M		2015-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.979	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.4	48	100	0.118	0.122	0.999	20.39	13.816		188659		-3	37.223

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.5	100		0.609	0.633	0.931	5.51	13.323

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	SAD	THROUGHOUT	2.4	48	93137	4902	99.97	0.2145	0.2134	0.22	0.2336	0.24	RANDOM	31.291

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]
0.05			-0.26		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.168
r_dihedral_angle_4_deg	13.361
r_dihedral_angle_3_deg	10.694
r_dihedral_angle_1_deg	5.534
r_angle_refined_deg	1.104
r_angle_other_deg	0.889
r_chiral_restr	0.066
r_bond_other_d	0.021
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.168
r_dihedral_angle_4_deg	13.361
r_dihedral_angle_3_deg	10.694
r_dihedral_angle_1_deg	5.534
r_angle_refined_deg	1.104
r_angle_other_deg	0.889
r_chiral_restr	0.066
r_bond_other_d	0.021
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11925
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms

Software

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