8AXY

Staphylococcus aureus endonuclease IV orthorhombic crystal form

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	- 0.1 M HEPES pH 7.0 - 2.2 M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.857	α = 90
b = 82.581	β = 90
c = 105.091	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 16M		2021-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.800	Diamond	I04

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	1.05	52.545	99.1	0.063	1	14.2	7.2		156665

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	1.05	1.07	95.8		1.882	0.319	0.5	6.1

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1xp3	1.05	52.545	156428	7783	98.942	0.137	0.1358	0.1577	15.324

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]
-0.042			0.795		-0.754

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.184
r_dihedral_angle_4_deg	16.411
r_dihedral_angle_3_deg	12.21
r_dihedral_angle_1_deg	6.01
r_lrange_it	4.006
r_lrange_other	2.993
r_scangle_it	2.187
r_scangle_other	1.978
r_scbond_it	1.685
r_angle_refined_deg	1.566
r_mcangle_it	1.566
r_mcangle_other	1.566
r_scbond_other	1.562
r_angle_other_deg	1.505
r_rigid_bond_restr	1.488
r_mcbond_it	1.126
r_mcbond_other	1.124
r_nbd_refined	0.211
r_symmetry_nbd_refined	0.198
r_nbd_other	0.182
r_nbtor_refined	0.17
r_symmetry_nbd_other	0.169
r_symmetry_xyhbond_nbd_refined	0.153
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.085
r_xyhbond_nbd_other	0.023
r_bond_refined_d	0.012
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	2333
Nucleic Acid Atoms
Solvent Atoms	521
Heterogen Atoms	63

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MoRDa	phasing