9FQ2 | pdb_00009fq2

Poliovirus 3C protease in H32 spacegroup

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L1N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Shotgun ECO screen, well B9 1.6M Sodium citrate tribasic dihydrate

Crystal Properties
Matthews coefficient	Solvent content
2.93	57.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.734	α = 90
b = 122.734	β = 90
c = 158.698	γ = 120

Symmetry
Space Group	H 3 2

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 EIGER2 XE 16M		2024-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	2.37	63.585	99.91	1	19.1	20.6		18923

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	2.37	2.41			0.294

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	2.37	63.585	18906	923	99.989	0.196	0.1931	0.2	0.2579	0.26	80.791

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]
-0.298	-0.149		-0.298		0.968

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_other	20.228
r_lrange_it	20.217
r_dihedral_angle_2_deg	20.089
r_dihedral_angle_3_deg	19.072
r_scangle_it	17.891
r_scangle_other	17.887
r_mcangle_it	15.686
r_mcangle_other	15.682
r_dihedral_angle_6_deg	14.346
r_scbond_it	13.605
r_scbond_other	13.603
r_mcbond_it	12.315
r_mcbond_other	12.307
r_dihedral_angle_1_deg	9.59
r_angle_refined_deg	2.67
r_angle_other_deg	0.996
r_nbd_refined	0.207
r_ncsr_local_group_1	0.188
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.174
r_symmetry_nbd_refined	0.162
r_xyhbond_nbd_refined	0.157
r_nbd_other	0.152
r_symmetry_xyhbond_nbd_other	0.133
r_chiral_restr	0.124
r_symmetry_nbtor_other	0.09
r_symmetry_xyhbond_nbd_refined	0.032
r_bond_refined_d	0.013
r_gen_planes_refined	0.013
r_chiral_restr_other	0.007
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2719
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
REFMAC	phasing