9PI5 | pdb_00009pi5

Poly dA bound form of Single stranded DNA-binding protein(ICP8) from Herpes simplex virus-1. Mutations: C254S, C455S

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	0.02 M magnesium chloride, 0.05 M PIPES, pH 7.5, 4% PEG8000, 0.001 M spermine

Crystal Properties
Matthews coefficient	Solvent content
4.12	70.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.171	α = 90
b = 151.171	β = 90
c = 154.561	γ = 120

Symmetry
Space Group	P 32 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		2022-06-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.979330	NSLS-II	17-ID-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	3	154.56	100	0.053	0.998	11.7	1.9		41340

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.12	100		0.828	0.312	1

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3	130.918	41302	2119	99.978	0.202	0.1997	0.2055	0.2377	0.2546	RANDOM	37.108

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]
-3.536	-1.768		-3.536		11.469

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.444
r_dihedral_angle_6_deg	14.169
r_lrange_it	9.147
r_lrange_other	9.147
r_dihedral_angle_1_deg	8.262
r_scangle_it	5.026
r_scangle_other	5.025
r_mcangle_it	4.524
r_mcangle_other	4.523
r_scbond_it	2.995
r_scbond_other	2.994
r_mcbond_it	2.678
r_mcbond_other	2.678
r_angle_refined_deg	1.353
r_angle_other_deg	0.462
r_nbd_refined	0.246
r_nbd_other	0.202
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.162
r_symmetry_xyhbond_nbd_refined	0.135
r_symmetry_nbd_refined	0.129
r_symmetry_nbtor_other	0.081
r_symmetry_xyhbond_nbd_other	0.072
r_chiral_restr	0.059
r_dihedral_angle_other_2_deg	0.026
r_ext_dist_refined_b	0.024
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8052
Nucleic Acid Atoms	168
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB-REDO	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing