2P3B | pdb_00002p3b

Crystal Structure of the subtype B wild type HIV protease complexed with TL-3 inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Crystal Structure of the multi-drug resistant mutant subtype B HIV protease complexed with TL-3 inhibitor

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	277	15% saturated ammonium sulfate solution, 6% (v/v) MPD, 85mM sodium citrate/170mM sodium phosphate, 0.02% sodium azide, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.164	α = 90
b = 63.164	β = 90
c = 83.414	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	298	IMAGE PLATE	MAR scanner 345 mm plate	MIRRORS	1998-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.1	54.72	99.7	0.075	13.6	3.7		11047

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.21	100		0.414	2.7	3.7	1587

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	Crystal Structure of the multi-drug resistant mutant subtype B HIV protease complexed with TL-3 inhibitor	2.1	16.58	11011	1084	99.82	0.165	0.159	0.1591	0.219	0.2183	RANDOM	31.322

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]
0.04	0.02		0.04		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.853
r_dihedral_angle_4_deg	18.41
r_dihedral_angle_3_deg	17.262
r_sphericity_bonded	13.27
r_dihedral_angle_1_deg	6.534
r_scangle_it	3.911
r_mcangle_it	2.84
r_scbond_it	2.785
r_rigid_bond_restr	1.947
r_mcbond_it	1.638
r_angle_refined_deg	1.575
r_nbtor_refined	0.32
r_xyhbond_nbd_refined	0.23
r_nbd_refined	0.222
r_symmetry_vdw_refined	0.172
r_symmetry_hbond_refined	0.111
r_chiral_restr	0.085
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1520
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	66

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
PHASER	phasing