3DLR

Crystal structure of the catalytic core domain from PFV integrase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1CXU	PDB ENTRY 1cxu

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	1.0 M ammonium formate, 0.2 M magnesium cloride, 5 mM dithiotreitol, 0.1 M 2-(N-morpholino)ethanesulfonic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.14	α = 90
b = 52.14	β = 90
c = 239.78	γ = 120

Symmetry
Space Group	P 61 2 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	MARMOSAIC 225 mm CCD		2008-01-26	M	SINGLE WAVELENGTH
2	1	x-ray		CCD	MARMOSAIC 225 mm CCD		2008-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.95373	ESRF	BM14
2	SYNCHROTRON	ESRF BEAMLINE BM14	0.97837	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.2	45.18	99.5	0.105	17.4	8.9	10584	10584			32.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.2	2.32	99.3		0.681	3.4	9.3	1477

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	SAD	THROUGHOUT	PDB ENTRY 1cxu	2.2	45.18	9540	1042	99.2	0.21394	0.20905	0.25922	RANDOM	32.046

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]
0.82	0.41		0.82		-1.23

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_2_deg	35.371
f_dihedral_angle_4_deg	16.931
f_dihedral_angle_3_deg	16.041
f_dihedral_angle_1_deg	5.838
f_scangle_it	2.472
f_scbond_it	1.746
f_angle_refined_deg	1.122
f_mcangle_it	1.025
f_mcbond_it	0.558
f_nbtor_refined	0.307
f_nbd_refined	0.197
f_symmetry_vdw_refined	0.149
f_symmetry_hbond_refined	0.131
f_xyhbond_nbd_refined	0.114
f_metal_ion_refined	0.099
f_chiral_restr	0.073
f_bond_refined_d	0.01
f_gen_planes_refined	0.004
f_bond_other_d
f_angle_other_deg
f_gen_planes_other
f_nbd_other
f_nbtor_other
f_xyhbond_nbd_other
f_metal_ion_other
f_symmetry_vdw_other
f_symmetry_hbond_other
f_symmetry_metal_ion_refined
f_symmetry_metal_ion_other
f_mcbond_other
f_rigid_bond_restr
f_sphericity_free
f_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1241
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	1

Software

Software
Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
REFMAC	refinement