9PI3 | pdb_00009pi3

Single stranded DNA-binding protein (ICP8) from Herpes simplex virus-1, apo form. Mutations: C254S, C455S, K769A, E770A

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	2% PEG 8,000, 50mM HEPES, pH 7.5, 40mM MgCl2, 2mM DTT, 1mM Spermine

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.99	α = 90
b = 140.2	β = 111.06
c = 98.8	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	100	PIXEL	DECTRIS EIGER X 9M		2023-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.920085	NSLS-II	17-ID-1

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	2.75	92.2	100	0.238	0.983	7.5	6.9		59439

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	2.75	2.85			1.03	0.735	2.5

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	2.75	92.2	59411	2968	99.988	0.188	0.1837	0.189	0.263	0.2637	RANDOM	36.627

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]
1.875		-0.146	-0.631		-0.873

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.156
r_dihedral_angle_6_deg	14.751
r_dihedral_angle_2_deg	13.343
r_lrange_it	8.718
r_lrange_other	8.718
r_dihedral_angle_1_deg	6.776
r_scangle_it	5.13
r_scangle_other	5.13
r_mcangle_it	4.695
r_mcangle_other	4.694
r_scbond_it	3.175
r_scbond_other	3.175
r_mcbond_it	2.901
r_mcbond_other	2.901
r_angle_refined_deg	1.614
r_angle_other_deg	0.532
r_symmetry_nbd_refined	0.239
r_nbd_refined	0.22
r_symmetry_nbd_other	0.204
r_nbtor_refined	0.184
r_nbd_other	0.165
r_xyhbond_nbd_refined	0.157
r_symmetry_xyhbond_nbd_refined	0.137
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.07
r_symmetry_xyhbond_nbd_other	0.07
r_chiral_restr_other	0.011
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16092
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing