2PC0

Apo Wild-type HIV Protease in the open conformation

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AZ8	pdb entry 2AZ8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.2	277	0.2 M Magnesium chloride, 20% w/v PEG 3350, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.416	α = 90
b = 46.416	β = 90
c = 101.37	γ = 90

Symmetry
Space Group	P 41 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	103	CCD	ADSC QUANTUM 210	Double-crystal monochromator, 1m long Rh coated bent cylindrical mirror for horizontal and vertical focusing	2006-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL1-5		SSRL	BL1-5

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	1.4	20.8	99	0.057	16.5	6.2	27866	22409		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.44	98		0.522	3	6.4	1588

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 2AZ8	1.4	20.8	22398	1165	98.68	0.155	0.153	0.186	RANDOM	15.554

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]
0.3			0.3		-0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.646
r_dihedral_angle_4_deg	18.353
r_dihedral_angle_3_deg	9.025
r_dihedral_angle_1_deg	6.325
r_scangle_it	5.026
r_scbond_it	3.752
r_mcangle_it	2.672
r_mcbond_it	2.151
r_mcbond_other	1.61
r_angle_refined_deg	1.196
r_angle_other_deg	0.593
r_chiral_restr	0.39
r_symmetry_vdw_other	0.317
r_nbd_refined	0.296
r_symmetry_vdw_refined	0.216
r_nbd_other	0.202
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.158
r_symmetry_hbond_refined	0.107
r_nbtor_other	0.086
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_gen_planes_other	0.002
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	760
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms	6

Software

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