6E9A | pdb_00006e9a

HIV-1 WILD TYPE PROTEASE WITH GRL-034-17A, (3aS, 5R, 6aR)-2-OXOHEXAHYD CYCLOPENTA[D]-5-OXAZOLYL URETHANE WITH A BICYCLIC OXAZOLIDINONE SCAFF AS THE P2 LIGAND

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NU3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8	298	1.00M NACL, 0.1M SODIUM ACETATE PH 4.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.372	α = 90
b = 86.276	β = 90
c = 46.02	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	100	PIXEL	DECTRIS EIGER X 16M		2018-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

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	1.22	50	91.6	0.099	16.1	5.3		64157

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	1.22	1.26	51.2		0.351	2.4	2

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 (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	FREE R-VALUE	3NU3	1.22	50	64073	64073	3168	91.7	0.1553	0.1536	0.16	0.1883	0.19	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
71		1703.4

RMS Deviations
Key	Refinement Restraint Deviation
s_approx_iso_adps	0.0992
s_non_zero_chiral_vol	0.0826
s_zero_chiral_vol	0.0735
s_similar_adp_cmpnt	0.0518
s_angle_d	0.0315
s_anti_bump_dis_restr	0.0302
s_bond_d	0.0124
s_from_restr_planes	0.0046
s_similar_dist
s_rigid_bond_adp_cmpnt

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1512
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms	40

Software

Software
Software Name	Purpose
SHELXL-97	refinement
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.