1ZBG | pdb_00001zbg

Crystal structure of a complex of mutant hiv-1 protease (A71V, V82T, I84V) with a hydroxyethylamine peptidomimetic inhibitor BOC-PHE-PSI[R-CH(OH)CH2NH]-PHE-GLU-PHE-NH2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1A9M	PDB ENTRY 1A9M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.4	298	0.1 M Na Citrate, 1M NaCl, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.409	α = 90
b = 87.419	β = 90
c = 94.9	γ = 90

Symmetry
Space Group	I 2 2 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	MARRESEARCH	microfocussing mirrors - testing	2000-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934	ESRF	ID14-1

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	1.995	25	87.6	0.061	0.061	19.4	3.2	16342	14316		-999	34

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	1.995	2.047	86.4		0.325	0.325	3.9	3	997

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1A9M	1.995	25	14316	14316	739	87.6	0.18498	0.18498	0.18665	0.19	0.23732	0.19	RANDOM	31.629

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]
-1.43			-2.97		4.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.74
r_dihedral_angle_3_deg	16.185
r_dihedral_angle_4_deg	15.259
r_dihedral_angle_1_deg	6.78
r_scangle_it	4.224
r_scbond_it	2.627
r_mcangle_it	1.822
r_angle_refined_deg	1.697
r_mcbond_it	1.035
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.74
r_dihedral_angle_3_deg	16.185
r_dihedral_angle_4_deg	15.259
r_dihedral_angle_1_deg	6.78
r_scangle_it	4.224
r_scbond_it	2.627
r_mcangle_it	1.822
r_angle_refined_deg	1.697
r_mcbond_it	1.035
r_nbtor_refined	0.315
r_symmetry_hbond_refined	0.249
r_nbd_refined	0.213
r_symmetry_vdw_refined	0.197
r_xyhbond_nbd_refined	0.157
r_chiral_restr	0.133
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1526
Nucleic Acid Atoms
Solvent Atoms	159
Heterogen Atoms	55

Software

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

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.