3EKT | pdb_00003ekt

Crystal Structure of the inhibitor Darunavir (DRV) in complex with a multi-drug resistant HIV-1 protease variant (L10F/G48V/I54V/V64I/V82A) (Refer: FLAP+ in citation.)

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	298	Refer citation, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3	58.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.013	α = 90
b = 92.013	β = 90
c = 106.161	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	133	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	1.97	40	95.8	0.05	15.4		34578	34578

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.97	40	34447	1713	95.59	0.211	0.209	0.22	0.258	0.24	RANDOM	13.827

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]
0.39	0.19		0.39		-0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.761
r_dihedral_angle_4_deg	15.716
r_dihedral_angle_3_deg	13.938
r_dihedral_angle_1_deg	6.67
r_scangle_it	2.424
r_scbond_it	1.711
r_angle_refined_deg	1.12
r_angle_other_deg	1.06
r_mcangle_it	0.987
r_mcbond_it	0.897
r_symmetry_hbond_refined	0.255
r_nbd_other	0.224
r_xyhbond_nbd_refined	0.217
r_symmetry_vdw_refined	0.203
r_symmetry_vdw_other	0.2
r_nbd_refined	0.195
r_xyhbond_nbd_other	0.182
r_nbtor_refined	0.181
r_mcbond_other	0.116
r_nbtor_other	0.087
r_chiral_restr	0.074
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2948
Nucleic Acid Atoms
Solvent Atoms	321
Heterogen Atoms	133

Software

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