2NPH

Crystal structure of HIV1 protease in situ product complex

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	298	Ammonium Sulfate precipitant, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.03	α = 90
b = 62.03	β = 90
c = 81.78	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					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.97945	ESRF	BM30A

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	1.65	32.53	97	0.081	0.081	10.16	5.53	20957	20326			39.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.65	32.53	20957	20326	1069	100	0.216	0.216	0.214	0.259	RANDOM	33.426

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]
0.36	0.18		0.36		-0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.938
r_dihedral_angle_4_deg	14.582
r_dihedral_angle_3_deg	12.526
r_dihedral_angle_1_deg	5.207
r_scangle_it	4.892
r_scbond_it	2.941
r_mcangle_it	1.945
r_angle_refined_deg	1.546
r_mcbond_it	1.16
r_symmetry_hbond_refined	0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.938
r_dihedral_angle_4_deg	14.582
r_dihedral_angle_3_deg	12.526
r_dihedral_angle_1_deg	5.207
r_scangle_it	4.892
r_scbond_it	2.941
r_mcangle_it	1.945
r_angle_refined_deg	1.546
r_mcbond_it	1.16
r_symmetry_hbond_refined	0.76
r_nbtor_refined	0.331
r_symmetry_vdw_refined	0.288
r_xyhbond_nbd_refined	0.283
r_nbd_refined	0.253
r_chiral_restr	0.104
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1585
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
XDS	data scaling
CNS	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.