3GI4

Crystal structure of protease inhibitor, KB60 in complex with wild type HIV-1 protease

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.2	298	126 mM sodium phosphate pH 6.2, 63 mM sodium citrate, 24-29% ammonium sulphate, vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.809	α = 90
b = 58.131	β = 90
c = 61.568	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	200	IMAGE PLATE	RIGAKU RAXIS IV			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	1.85	50	99.7	0.06		6.6		16121

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	1.85	1.92	97.4		0.319		4.7	1547

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		THROUGHOUT	1.85	25.23	16079	808	99.57	0.172	0.169	0.221	RANDOM	24.766

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]
-0.76			-0.01		0.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.748
r_dihedral_angle_4_deg	15.18
r_dihedral_angle_3_deg	10.141
r_dihedral_angle_1_deg	6.041
r_scangle_it	1.52
r_angle_refined_deg	1.403
r_scbond_it	0.997
r_mcangle_it	0.747
r_angle_other_deg	0.698
r_mcbond_it	0.527
r_symmetry_hbond_refined	0.204
r_nbd_other	0.18
r_nbd_refined	0.175
r_symmetry_vdw_other	0.167
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.132
r_mcbond_other	0.109
r_symmetry_vdw_refined	0.09
r_nbtor_other	0.079
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1486
Nucleic Acid Atoms
Solvent Atoms	139
Heterogen Atoms	65

Software

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