10HO | pdb_000010ho

Crystal structure of alkaline nuclease from Herpes simplex virus-1

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	277.15	Ammonium sulfate, Sodium acetate, PEG 4000, Glycerol and DMSO

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.997	α = 90
b = 80.233	β = 90
c = 127.572	γ = 90

Symmetry
Space Group	P 21 21 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 EIGER X 9M	KB bimorph mirrors	2024-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.92010	NSLS-II	17-ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.46	29.642	99.9	0.037	0.052	0.037	0.999	13.8	1.9		22700

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.46	2.56	99.2		0.316	0.316	0.446	0.885	2.4	1.9

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.46	29.642	22644	1104	99.876	0.184	0.1809	0.182	0.2378	0.2395	61.938

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]
7.233			-3		-4.233

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.509
r_dihedral_angle_6_deg	14.39
r_lrange_other	14.004
r_lrange_it	13.989
r_scangle_it	12.458
r_scangle_other	12.399
r_dihedral_angle_2_deg	10.319
r_mcangle_it	10.024
r_mcangle_other	10.021
r_scbond_it	8.945
r_scbond_other	8.84
r_dihedral_angle_1_deg	7.319
r_mcbond_other	7.299
r_mcbond_it	7.298
r_angle_refined_deg	2.247
r_angle_other_deg	0.754
r_symmetry_nbd_refined	0.326
r_nbd_refined	0.229
r_symmetry_nbd_other	0.206
r_nbtor_refined	0.192
r_symmetry_xyhbond_nbd_other	0.185
r_nbd_other	0.151
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.09
r_symmetry_xyhbond_nbd_refined	0.038
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3317
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms	18

Software

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