3BVP

Crystal Structure of the N-terminal Catalytic Domain of TP901-1 Integrase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	294	PEG8000, Mg(OAc)2, pH 6.0, vapor diffusion, hanging drop, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.12	60.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.229	α = 90
b = 67.229	β = 90
c = 174.565	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4		2007-07-08	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315		2007-07-08	M	MAD
3	1	x-ray	100	CCD	ADSC QUANTUM 315		2007-07-09	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.0093	ALS	8.2.1
2	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.9200, 0.9203, 0.9099	ALS	8.2.1
3	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.0722, 1.0726, 1.0540	ALS	8.2.1

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
1,2,3	2.1	50	96.4	0.056	15.8	8.1		23563

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)
1,2,3	2.1	2.18	77.8		0.44		5.1	1863

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.1	44	23494	1195	96.44	0.201	0.198	0.263	RANDOM	64.09

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]
1.93			1.93		-3.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.652
r_dihedral_angle_4_deg	19.979
r_dihedral_angle_3_deg	16.294
r_dihedral_angle_1_deg	4.846
r_mcangle_it	1.475
r_scangle_it	1.436
r_angle_refined_deg	1.212
r_scbond_it	0.949
r_mcbond_it	0.912
r_nbtor_refined	0.306
r_nbd_refined	0.211
r_symmetry_vdw_refined	0.186
r_xyhbond_nbd_refined	0.175
r_symmetry_hbond_refined	0.135
r_chiral_restr	0.09
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2132
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction