2NXD | pdb_00002nxd

Structure of HIV-1 protease D25N complexed with rt-rh analogue peptide GLY-ALA-ASP-ILE-PHE*TYR-LEU-ASP-GLY-ALA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1T3R	1T3R - Crystal structure of HIV-1 protease complexed with the inhibitor TMC114

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	298	126 mM sodium phosphate pH 6.2; 63mM sodium citrate; 25-35%Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2	38.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.171	α = 90
b = 57.692	β = 90
c = 61.482	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	200	IMAGE PLATE	RIGAKU RAXIS IV	Yale Mirrors	2005-03-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	2	42.07	92.7	0.034	0.034	21.2	5	11909	11909

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1T3R - Crystal structure of HIV-1 protease complexed with the inhibitor TMC114	2	42.07	11295	11295	586	92.82	0.1979	0.1979	0.19505	0.25737	RANDOM	46.962

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]
-0.82			-0.8		1.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.513
r_dihedral_angle_4_deg	16.62
r_dihedral_angle_3_deg	14.756
r_dihedral_angle_1_deg	7.125
r_scangle_it	2.177
r_scbond_it	1.514
r_angle_refined_deg	1.218
r_mcangle_it	0.986
r_mcbond_it	0.786
r_angle_other_deg	0.678
r_symmetry_vdw_other	0.198
r_nbd_other	0.19
r_nbd_refined	0.188
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.167
r_mcbond_other	0.163
r_symmetry_vdw_refined	0.15
r_symmetry_hbond_refined	0.144
r_nbtor_other	0.081
r_chiral_restr	0.072
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1540
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms

Software

Software
Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling