Experiment: 2B4J

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BIS	PDB Entry: 1BIS (Integrase), 1Z9E (LEDGF)
experimental model	PDB	1Z9E	PDB Entry: 1BIS (Integrase), 1Z9E (LEDGF)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.25	295	PEG-3350, Na2HPO4, NaH2PO4, KH2PO4, NACL, HEPES, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.421	α = 90
b = 60.593	β = 109.06
c = 71.126	γ = 90

Symmetry
Space Group	C 1 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	CCD	ADSC QUANTUM 4		2005-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	1.00	NSLS	X26C

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	2.02	50	99.2	0.072	18.9	4.8	32648	32136	3.1	3.1	35.2

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	2.02	2.09	99.2	99.2	0.47	3.1	4.5

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB Entry: 1BIS (Integrase), 1Z9E (LEDGF)	2.02	20	30406	32113	1627	99.19	0.183	0.183	0.181	0.226	RANDOM	37.386

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		1.3	-0.38		1.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.69
r_dihedral_angle_4_deg	19.538
r_dihedral_angle_3_deg	15.922
r_dihedral_angle_1_deg	5.524
r_scangle_it	4.361
r_scbond_it	2.778
r_angle_refined_deg	1.602
r_mcangle_it	1.6
r_mcbond_it	0.981
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.69
r_dihedral_angle_4_deg	19.538
r_dihedral_angle_3_deg	15.922
r_dihedral_angle_1_deg	5.524
r_scangle_it	4.361
r_scbond_it	2.778
r_angle_refined_deg	1.602
r_mcangle_it	1.6
r_mcbond_it	0.981
r_nbtor_refined	0.301
r_symmetry_hbond_refined	0.237
r_nbd_refined	0.213
r_symmetry_vdw_refined	0.179
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.132
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3503
Nucleic Acid Atoms
Solvent Atoms	220
Heterogen Atoms	34

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
CCP4	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.