8F0F | pdb_00008f0f

HIV-1 wild type protease with GRL-110-19A, a chloroacetamide derivative based on Darunavir as P2' group

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6VOD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	0.65 M NaCl, 0.1 M Sodium Acetate, pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.419	α = 90
b = 86.235	β = 90
c = 46.075	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	CCD	RAYONIX MX300-HS		2019-12-11	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.29	50	95.4	0.052	0.057	0.021	14.5	6.8		56469

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.29	1.34	69.8		0.639	0.739	0.358	0.704		3.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	6VOD	1.29	34.72	53658	2771	95.28	0.1331	0.1316	0.13	0.1626	0.16	RANDOM	14.078

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]
-0.15			-0.46		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.893
r_dihedral_angle_1_deg	6.941
r_dihedral_angle_2_deg	5.041
r_rigid_bond_restr	4.802
r_angle_refined_deg	1.926
r_angle_other_deg	0.677
r_chiral_restr	0.133
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.893
r_dihedral_angle_1_deg	6.941
r_dihedral_angle_2_deg	5.041
r_rigid_bond_restr	4.802
r_angle_refined_deg	1.926
r_angle_other_deg	0.677
r_chiral_restr	0.133
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.008
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1512
Nucleic Acid Atoms
Solvent Atoms	227
Heterogen Atoms	92

Software

Software
Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.