9BCY | pdb_00009bcy

Crystal structure of Mayaro virus capsid C-terminal domain

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	291	22% PEG 3350, 100mM Bis-Tris pH 7.2

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.16	α = 93.585
b = 40.112	β = 94.403
c = 56.511	γ = 111.925

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	PIXEL	DECTRIS PILATUS 2M		2021-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS SIRIUS BEAMLINE MANACA	0.9772	LNLS SIRIUS	MANACA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.18	37.057	93.08	0.05812	0.06895	0.03665	0.994	16.96	3.6		96920			9.59

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.18	1.222			0.09189	0.1084	0.05683	0.988	10.72

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.18	37.057	96920	4894	93.087	0.166	0.1648	0.1734	0.1806	0.19	13.381

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]
0.459	-0.115	0.046	-0.15	-0.048	-0.156

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.195
r_lrange_other	16.364
r_lrange_it	16.096
r_dihedral_angle_4_deg	15.888
r_scangle_it	11.855
r_scangle_other	11.851
r_mcangle_it	11.613
r_mcangle_other	11.611
r_dihedral_angle_3_deg	9.248
r_scbond_it	9.002
r_scbond_other	8.999
r_dihedral_angle_1_deg	7.459
r_mcbond_it	7.402
r_mcbond_other	7.4
r_angle_refined_deg	1.786
r_angle_other_deg	1.747
r_nbd_refined	0.224
r_symmetry_nbd_other	0.211
r_nbd_other	0.19
r_nbtor_refined	0.179
r_symmetry_nbd_refined	0.156
r_xyhbond_nbd_refined	0.128
r_symmetry_xyhbond_nbd_refined	0.118
r_chiral_restr	0.106
r_symmetry_nbtor_other	0.082
r_gen_planes_other	0.032
r_bond_other_d	0.018
r_bond_refined_d	0.016
r_gen_planes_refined	0.016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2286
Nucleic Acid Atoms
Solvent Atoms	489
Heterogen Atoms	32

Software

Software
Software Name	Purpose
MxCuBE	data collection
XDS	data reduction
SCALA	data scaling
BALBES	phasing
REFMAC	refinement
PDB-REDO	refinement