3HLO | pdb_00003hlo

Crystal structure of chemically synthesized 'covalent dimer' [Gly51/D-Ala51']HIV-1 protease

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	0.1 M citrate, 0.2 M sodium phosphate, 30% (v/v) ammonium sulfate, 10% (v/v) DMSO, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.341	α = 90
b = 58.059	β = 90
c = 61.368	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	110	CCD	ADSC QUANTUM 315	bent conical Si-mirror (Rh coating); bent Ge(111) monochromator	2007-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.90020	APS	14-BM-C

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	1.6	50	99.6	0.047	38.3	7.3	25025	24925

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	1.6	1.66	100		0.354	6.61	7.1	2450

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1.6	20	23692	23595	1263	99.59	0.18948	0.18777	0.2035	0.22148	0.2285	RANDOM	25.329

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]
0.13					-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.538
r_dihedral_angle_4_deg	23.228
r_dihedral_angle_3_deg	13.254
r_dihedral_angle_1_deg	5.881
r_scangle_it	4.099
r_scbond_it	2.678
r_mcangle_it	1.889
r_angle_refined_deg	1.691
r_mcbond_it	1.217
r_nbtor_refined	0.316

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.538
r_dihedral_angle_4_deg	23.228
r_dihedral_angle_3_deg	13.254
r_dihedral_angle_1_deg	5.881
r_scangle_it	4.099
r_scbond_it	2.678
r_mcangle_it	1.889
r_angle_refined_deg	1.691
r_mcbond_it	1.217
r_nbtor_refined	0.316
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.174
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.126
r_symmetry_hbond_refined	0.116
r_bond_refined_d	0.016
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1544
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	53

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.