4LL3

Structure of wild-type HIV protease in complex with darunavir

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				RESERVOIR: 2 M SODIUM FORMATE, 0.1 M SODIUM ACETATE, PH 4.6. DROPS: 2 UL PROTEIN + 1UL RESERVOIR, PROTEIN CONCENTRATION 5MG/ML, 5-FOLD MOLAR EXCESS OF INHIBITOR (DISSOLVED IN DMSO) OVER PROTEIN, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.557	α = 90
b = 62.557	β = 90
c = 81.523	γ = 120

Symmetry
Space Group	P 61

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		2009-05-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X12		EMBL/DESY, HAMBURG	X12

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	50	99.9	0.06	26.45	6.7		13257

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	2.02	99.9		0.513	2.7	5.1

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.95	27.09	12558	662	99.95	0.18523	0.18288	0.23	RANDOM	36.773

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]
-0.23	-0.11		-0.23		0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.981
r_dihedral_angle_4_deg	18.813
r_dihedral_angle_3_deg	14.079
r_dihedral_angle_1_deg	6.332
r_scangle_it	3.084
r_scbond_it	1.908
r_angle_refined_deg	1.508
r_mcangle_it	1.301
r_mcbond_it	1.296
r_nbtor_refined	0.314
r_symmetry_vdw_refined	0.233
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.171
r_symmetry_hbond_refined	0.134
r_chiral_restr	0.1
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1520
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	76

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling