8XY2 | pdb_00008xy2

Crystal structure of MPXV P1 protein S87P mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8XY1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	14.4% w/v PEG 8000, 80 mM Sodium cacodylate/ Hydrochloric acid pH 6.5, 160 mM Calcium acetate, 20% v/v Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.366	α = 90
b = 155.5	β = 90
c = 131.736	γ = 90

Symmetry
Space Group	C 2 2 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		2023-12-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97861	SSRF	BL19U1

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	2.24	43.91	99.9	0.999	11.1	6.5		29804

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	2.24	2.31			0.949

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	8XY1	2.24	42.461	29776	1502	99.923	0.221	0.2186	0.2223	0.2718	0.2682	40.64

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]
3.581			-0.975		-2.605

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.22
r_dihedral_angle_4_deg	14.424
r_dihedral_angle_3_deg	14.312
r_lrange_it	8.429
r_lrange_other	8.402
r_scangle_it	6.804
r_scangle_other	6.803
r_dihedral_angle_1_deg	6.189
r_mcangle_it	5.421
r_mcangle_other	5.42
r_scbond_it	4.59
r_scbond_other	4.589
r_mcbond_it	3.847
r_mcbond_other	3.845
r_angle_refined_deg	1.529
r_angle_other_deg	1.369
r_symmetry_xyhbond_nbd_refined	0.242
r_nbd_refined	0.212
r_nbd_other	0.192
r_xyhbond_nbd_refined	0.191
r_symmetry_nbd_other	0.181
r_nbtor_refined	0.168
r_symmetry_xyhbond_nbd_other	0.159
r_ncsr_local_group_2	0.102
r_ncsr_local_group_3	0.098
r_symmetry_nbd_refined	0.087
r_ncsr_local_group_4	0.087
r_chiral_restr	0.086
r_ncsr_local_group_1	0.079
r_ncsr_local_group_6	0.078
r_ncsr_local_group_5	0.077
r_symmetry_nbtor_other	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3875
Nucleic Acid Atoms
Solvent Atoms	392
Heterogen Atoms

Software

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