8P61 | pdb_00008p61

Crystal structure of O'nyong'nyong virus capsid protease (106-256)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5H23

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	0.1 M sodium cacodylate (pH 6.5), 2.2 M ammonium sulfate and 100 mM ethylenediaminetetraacetic acid disodium salt Crystals were cryoprotected in 25% (v/v) glycerol in the reservoir solution and flash-cooled in liquid nitrogen

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.65	α = 90
b = 112.13	β = 89.97
c = 67.1	γ = 90

Symmetry
Space Group	C 1 2 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 EIGER X 16M		2022-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

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	1.9	48.46	98.9	0.961	2.5	1.7		51622

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.94			0.157	0.6

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	1.9	44.865	51597	2100	98.868	0.227	0.2253	0.23	0.268	0.27	42.13

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]
-3.036		0.52	-1.658		4.694

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.445
r_dihedral_angle_3_deg	15.509
r_dihedral_angle_2_deg	12.157
r_lrange_it	11.721
r_lrange_other	11.593
r_scangle_it	8.667
r_scangle_other	8.427
r_dihedral_angle_1_deg	8.186
r_mcangle_other	5.987
r_mcangle_it	5.986
r_scbond_it	5.63
r_scbond_other	5.431
r_mcbond_it	4.069
r_mcbond_other	4.046
r_angle_refined_deg	1.588
r_angle_other_deg	0.609
r_xyhbond_nbd_refined	0.181
r_nbd_refined	0.163
r_symmetry_nbd_other	0.161
r_nbtor_refined	0.161
r_ncsr_local_group_3	0.15
r_ncsr_local_group_5	0.149
r_nbd_other	0.141
r_ncsr_local_group_2	0.129
r_ncsr_local_group_4	0.126
r_ncsr_local_group_6	0.125
r_symmetry_nbd_refined	0.108
r_symmetry_xyhbond_nbd_refined	0.093
r_ncsr_local_group_1	0.08
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.074
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_symmetry_xyhbond_nbd_other	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4514
Nucleic Acid Atoms
Solvent Atoms	262
Heterogen Atoms	84

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing