8XY1 | pdb_00008xy1

Crystal structure of MPXV P1 protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I39

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.8 M Succinic acid, pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.417	α = 90
b = 114.417	β = 90
c = 126.789	γ = 120

Symmetry
Space Group	P 3 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 PILATUS 6M		2023-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.979152	SSRF	BL02U1

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	2.57	99.09	100	0.998	10.9	16		30914

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	2.57	2.71			0.74

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	THROUGHOUT	2I39	2.575	99	30763	1489	99.46	0.198	0.1961	0.2013	0.2418	0.2492	50.587

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]
0.752	0.376		0.752		-2.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.408
r_dihedral_angle_4_deg	21.195
r_dihedral_angle_3_deg	16.255
r_lrange_other	11.998
r_lrange_it	11.994
r_scangle_it	10.009
r_scangle_other	10.008
r_mcangle_it	6.775
r_mcangle_other	6.775
r_scbond_it	6.604
r_scbond_other	6.603
r_dihedral_angle_1_deg	5.346
r_mcbond_it	4.712
r_mcbond_other	4.709
r_angle_refined_deg	1.597
r_angle_other_deg	1.371
r_nbd_other	0.233
r_nbd_refined	0.211
r_symmetry_nbd_refined	0.188
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.163
r_ncsr_local_group_3	0.095
r_ncsr_local_group_13	0.091
r_ncsr_local_group_15	0.091
r_chiral_restr	0.088
r_ncsr_local_group_5	0.088
r_ncsr_local_group_10	0.088
r_ncsr_local_group_7	0.087
r_ncsr_local_group_12	0.085
r_ncsr_local_group_6	0.083
r_ncsr_local_group_8	0.081
r_ncsr_local_group_14	0.081
r_symmetry_nbtor_other	0.078
r_ncsr_local_group_9	0.076
r_ncsr_local_group_1	0.072
r_ncsr_local_group_11	0.067
r_ncsr_local_group_4	0.064
r_ncsr_local_group_2	0.059
r_symmetry_xyhbond_nbd_refined	0.045
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5840
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms

Software

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