8WF7

The Crystal Structure of integrase from Biortus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7UOQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	100mM sodium acetate at pH 5.3, 1.9M ammonium

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.027	α = 90
b = 71.027	β = 90
c = 66.849	γ = 120

Symmetry
Space Group	P 31 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 9M		2022-12-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.953743	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.55	45.306	100	0.08	19.1	15.1		28716

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58	100		0.853	3.2

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.55	45.306	28716	1449	99.979	0.177	0.1761	0.1986	25.388

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]
0.086	0.043		0.086		-0.278

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.672
r_dihedral_angle_3_deg	11.426
r_lrange_it	6.611
r_lrange_other	6.395
r_dihedral_angle_2_deg	6.15
r_dihedral_angle_1_deg	5.803
r_scangle_it	4.329
r_scangle_other	4.326
r_mcangle_it	3.057
r_mcangle_other	3.055
r_scbond_it	2.766
r_scbond_other	2.764
r_mcbond_other	1.908
r_mcbond_it	1.907
r_angle_refined_deg	1.219
r_angle_other_deg	0.419
r_nbd_refined	0.235
r_nbd_other	0.209
r_nbtor_refined	0.18
r_symmetry_nbd_other	0.173
r_symmetry_nbd_refined	0.17
r_xyhbond_nbd_refined	0.165
r_symmetry_xyhbond_nbd_refined	0.159
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.057
r_symmetry_xyhbond_nbd_other	0.036
r_gen_planes_refined	0.007
r_bond_refined_d	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	1179
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms	34

Software

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