4U7Q | pdb_00004u7q

Structure of wild-type HIV protease in complex with photosensitive inhibitor PDI-6

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	291	200mM LiCl, 20% PEG 1000

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.841	α = 90
b = 62.841	β = 90
c = 80.486	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	CCD	MARMOSAIC 225 mm CCD		2012-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.61	10	99.7	0.04	0.045	20.76	5.1		23062		-3	32.025

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.61	1.71	99.8		0.635	0.711	2.57

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	3NDW	1.7	10	19632	978	98.88	0.2775	0.2749	0.28	0.3262	0.29	RANDOM	34.869

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]
0.01			0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.118
r_dihedral_angle_3_deg	14.836
r_dihedral_angle_4_deg	14.786
r_dihedral_angle_1_deg	7.225
r_mcangle_it	4.576
r_mcbond_it	3.244
r_mcbond_other	3.233
r_angle_refined_deg	2.191
r_angle_other_deg	1.401
r_chiral_restr	0.122

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.118
r_dihedral_angle_3_deg	14.836
r_dihedral_angle_4_deg	14.786
r_dihedral_angle_1_deg	7.225
r_mcangle_it	4.576
r_mcbond_it	3.244
r_mcbond_other	3.233
r_angle_refined_deg	2.191
r_angle_other_deg	1.401
r_chiral_restr	0.122
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_bond_other_d	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1479
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms	114

Software

Software
Software Name	Purpose
XDS	data reduction
PDB_EXTRACT	data extraction
MOLREP	phasing
REFMAC	refinement
XSCALE	data scaling

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.