4EJD | pdb_00004ejd

HIV Protease (PR) dimer in closed form with pepstatin in active site and fragment 1F1 in the outside/top of flap

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	298	0.2 M potassium bromide, 0.2 M potassium thiocyanate, 3% PGA-LM, 3% MPD, 10% DMSO, 0.1 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 28.82	α = 90
b = 65.63	β = 90
c = 92.93	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 315r	Rh coated flat mirror	2010-06-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.979	SSRL	BL7-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.103	92.93	98.3	0.089	8.3	3.4	70609	70609

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	1.103	1.16	99.9		0.483	0.483	1.5	3.3	10342

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.103	18.96	70371	3543	97.77	0.1475	0.1459	0.1451	0.1762	0.1721	RANDOM	14.7297

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]
-0.02			-0.01		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.956
r_sphericity_free	35.424
r_dihedral_angle_3_deg	14.202
r_dihedral_angle_4_deg	11.903
r_sphericity_bonded	10.978
r_rigid_bond_restr	10.33
r_dihedral_angle_1_deg	6.865
r_angle_other_deg	2.064
r_angle_refined_deg	1.442
r_chiral_restr	0.139

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.956
r_sphericity_free	35.424
r_dihedral_angle_3_deg	14.202
r_dihedral_angle_4_deg	11.903
r_sphericity_bonded	10.978
r_rigid_bond_restr	10.33
r_dihedral_angle_1_deg	6.865
r_angle_other_deg	2.064
r_angle_refined_deg	1.442
r_chiral_restr	0.139
r_gen_planes_refined	0.015
r_bond_refined_d	0.01
r_gen_planes_other	0.002
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1562
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	30

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection

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.