1TSU | pdb_00001tsu

CRYSTAL STRUCTURE OF DECAMER NCP1 SUBSTRATE PEPTIDE IN COMPLEX WITH WILD-TYPE D25N HIV-1 PROTEASE VARIANT

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MTR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	298	SODIUM PHOSPHATE, SODIUM CITRATE, AMMONIUM SULPHATE, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.058	α = 90
b = 57.731	β = 90
c = 61.495	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	220	IMAGE PLATE	RIGAKU RAXIS	OSMIC MIRRORS	2002-10-29	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)	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	42.26	94.1	0.092			10450	10450	-3	-3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1MTR	2.1	42.26	-3	9912	9912	493	93.93	0.20717	0.20587	0.23355	RANDOM	40.067

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]
-1			-0.34		1.34

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	9.961
r_scbond_it	7.225
r_mcangle_it	5.128
r_dihedral_angle_1_deg	4.286
r_mcbond_it	3.623
r_angle_refined_deg	1.462
r_xyhbond_nbd_refined	0.52
r_symmetry_vdw_refined	0.465
r_symmetry_hbond_refined	0.31
r_nbd_refined	0.248

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	9.961
r_scbond_it	7.225
r_mcangle_it	5.128
r_dihedral_angle_1_deg	4.286
r_mcbond_it	3.623
r_angle_refined_deg	1.462
r_xyhbond_nbd_refined	0.52
r_symmetry_vdw_refined	0.465
r_symmetry_hbond_refined	0.31
r_nbd_refined	0.248
r_chiral_restr	0.178
r_gen_planes_refined	0.017
r_bond_refined_d	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1526
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
AMoRE	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.