Experiment: 3KFN

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AZ8	HIV PR dimer generated from PDB entry 2AZ8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	277	0.5 M KSCN, 0.1 M MES-HCL, pH 7.0, 10% DMSO, VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.95	α = 90
b = 85.57	β = 90
c = 46.49	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	ADSC QUANTUM 315r	Rh coated flat mirror	2009-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.97946	SSRL	BL7-1

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	1.77	48.564	93.7	0.089	0.089	3	3.4	23368	21896			27.9

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	1.77	1.82	92.5		0.637	0.637	1.1	3.4	1574

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	HIV PR dimer generated from PDB entry 2AZ8	1.77	48.55	23368	21866	1136	92.58	0.217	0.214	0.274	RANDOM	32.903

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]
3.68			-1.94		-1.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.718
r_dihedral_angle_4_deg	20.329
r_dihedral_angle_3_deg	14.318
r_dihedral_angle_1_deg	6.461
r_scangle_it	4.955
r_scbond_it	3.357
r_mcangle_it	2.217
r_angle_refined_deg	1.884
r_mcbond_it	1.346
r_chiral_restr	0.145

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.718
r_dihedral_angle_4_deg	20.329
r_dihedral_angle_3_deg	14.318
r_dihedral_angle_1_deg	6.461
r_scangle_it	4.955
r_scbond_it	3.357
r_mcangle_it	2.217
r_angle_refined_deg	1.884
r_mcbond_it	1.346
r_chiral_restr	0.145
r_bond_refined_d	0.023
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1518
Nucleic Acid Atoms
Solvent Atoms	201
Heterogen Atoms	96

Software

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