8A8X | pdb_00008a8x

TRIM7 PRYSPRY in complex with a MNV1-NS3 peptide HDDFGLQ

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8A5L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	291.15	1 M DL-Malic Acid pH 5, 0.1 M BIS-TRIS Propane pH 6.3

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.252	α = 90
b = 53.668	β = 105.55
c = 73.595	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS EIGER2 XE 16M		2022-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	70.91	97.4	1	6.8	3.3		15418

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	2.43			0.6

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	8A5L	2.37	28.337	15418	712	97.33	0.192	0.1885	0.2	0.2637	0.27	28.428

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]
0.572		-2.211	-0.828		1.287

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.592
r_dihedral_angle_4_deg	21.409
r_dihedral_angle_3_deg	17.204
r_dihedral_angle_1_deg	8.867
r_lrange_it	5.952
r_lrange_other	5.952
r_scangle_it	4.407
r_scangle_other	4.407
r_mcangle_it	3.428
r_mcangle_other	3.427
r_scbond_it	2.855
r_scbond_other	2.855
r_mcbond_it	2.225
r_mcbond_other	2.224
r_angle_refined_deg	1.653
r_angle_other_deg	1.242
r_nbd_refined	0.193
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.154
r_nbd_other	0.146
r_symmetry_xyhbond_nbd_refined	0.134
r_symmetry_nbd_refined	0.113
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.07
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	2813
Nucleic Acid Atoms
Solvent Atoms	56
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing