4MQ3 | pdb_00004mq3

The 1.1 Angstrom Structure of Catalytic Core Domain of FIV Integrase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3F9K	PDB ENTRY 3f9k

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	293	0.2M Trimethylamine N-oxide, 0.1M Tris pH 8.5, 20% PEG MME 2000, VAPOR DIFFUSION, temperature 293K
2	VAPOR DIFFUSION	5.5	293	0.2M Ammonium acetate, 0.1M Bis-Tris pH 5.5, 25% PEG 3350, VAPOR DIFFUSION, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 28.254	α = 90
b = 66.643	β = 103.43
c = 32.619	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	103	PIXEL	DECTRIS PILATUS 6M	mirrors	2013-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918409	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.08	33.32	95.6	0.03	0.03	15.94	3.41	48083	47812	-3	-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.08	1.135	90.3		2.59

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3f9k	1.08	33.32	47812	45678	2405	95.48	0.14173	0.1399	0.14	0.1765	0.18	RANDOM	17.061

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]
0.17		0.05	0.07		-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	43.451
r_dihedral_angle_2_deg	38.13
r_sphericity_bonded	17.379
r_dihedral_angle_3_deg	12.373
r_rigid_bond_restr	8.439
r_dihedral_angle_1_deg	5.609
r_angle_refined_deg	1.942
r_chiral_restr	0.121
r_bond_refined_d	0.02
r_gen_planes_refined	0.013
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1009
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms

Software

Software
Software Name	Purpose
MxCuBE	data collection
BALBES	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling