4CF1 | pdb_00004cf1

Interrogating HIV integrase for compounds that bind- a SAMPL challenge

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5		THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.

Crystal Properties
Matthews coefficient	Solvent content
2.95	58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.282	α = 90
b = 71.282	β = 90
c = 66.702	γ = 120

Symmetry
Space Group	P 31

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 CCD		2009-08-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1		Australian Synchrotron	MX1

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	1.95	45.3	100	0.07	18.2	5.6		27634		1

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	1.95	2.06	100		0.41	3.9	5.5

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 (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 3ZSQ	1.95	35.65	26173	1397	99.83	0.18869	0.18762	0.19	0.20865	0.22	RANDOM	28.637

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]
0.03	0.03		0.03		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.254
r_dihedral_angle_4_deg	13.963
r_dihedral_angle_3_deg	13.007
r_long_range_B_refined	5.578
r_long_range_B_other	5.577
r_dihedral_angle_1_deg	5.116
r_scangle_other	3.561
r_mcangle_it	2.847
r_mcangle_other	2.846
r_scbond_it	2.136
r_scbond_other	2.135
r_mcbond_it	1.726
r_mcbond_other	1.705
r_angle_refined_deg	1.277
r_angle_other_deg	0.745
r_chiral_restr	0.06
r_bond_refined_d	0.006
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	2323
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms	124

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing