6S58

AvaII restriction endonuclease in the absence of nucleic acids

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	0.03 M CaCl2, 0.1 M MES/imidazole, pH 6.5, 12.5% v/v MPD, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350 (Morpheus screen A4 condition with MgCl2 eliminated).

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.231	α = 90
b = 102.733	β = 90.67
c = 121.197	γ = 90

Symmetry
Space Group	C 1 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		2019-01-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

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	2.35	53.3	99.9	0.099	0.119	0.065	0.99	5.5	3.3		37373			54

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.43	99.8		0.452	0.55	0.309	0.764	1.8	3.1

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6G3B	2.32	51.37	35320	1958	96.37	0.21848	0.21634	0.25827	RANDOM	71.422

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]
16.22		7.04	-30.14		13.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.71
r_dihedral_angle_4_deg	16.572
r_dihedral_angle_3_deg	14.925
r_long_range_B_refined	6.525
r_long_range_B_other	6.496
r_dihedral_angle_1_deg	5.581
r_mcangle_it	4.406
r_mcangle_other	4.405
r_scangle_other	4.105
r_mcbond_it	2.825
r_mcbond_other	2.825
r_scbond_it	2.547
r_scbond_other	2.547
r_angle_refined_deg	1.141
r_angle_other_deg	0.886
r_chiral_restr	0.064
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7252
Nucleic Acid Atoms
Solvent Atoms	97
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing
ARP/wARP	model building