2R38 | pdb_00002r38

I84V HIV-1 protease mutant in complex with a carbamoyl decorated pyrrolidine-based inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PWR	PDB entry 2PWR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	2,25M NaCl, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.652811	53.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.385	α = 90
b = 85.711	β = 90
c = 46.556	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	113	IMAGE PLATE	RIGAKU RAXIS IV		2006-08-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.81	30	97.8	0.07	0.07	16.2	3.6		21217			19.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.81	1.84	100		0.422	0.422	2.6	2.6	1056

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	AB INITIO	FREE R	PDB entry 2PWR	1.81	10	2	4	19934	19934	1051	93	0.2042	0.1828	0.1811	0.19	0.2379	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
	1566	1651

RMS Deviations
Key	Refinement Restraint Deviation
s_similar_adp_cmpnt	0.062
s_zero_chiral_vol	0.038
s_non_zero_chiral_vol	0.036
s_from_restr_planes	0.0251
s_angle_d	0.022
s_anti_bump_dis_restr	0.01
s_bond_d	0.006
s_similar_dist
s_rigid_bond_adp_cmpnt
s_approx_iso_adps

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1489
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	47

Software

Software
Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	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.