3SA8 | pdb_00003sa8

Crystal structure of wild-type HIV-1 protease in complex with KB83

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F7A	PDB ENTRY 1F7A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	HANGING DROP, VAPOR DIFFUSION	6.2	295	24-29% ammonium sulfate, 63 mM sodium citrate, 126 mM phosphate buffer, pH 6.2, HANGING DROP, VAPOR DIFFUSION, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.731	α = 90
b = 57.739	β = 90
c = 61.769	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	100	CCD	ADSC QUANTUM 4		2009-12-17		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C		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	1.5	50	97	0.048	13.3	6.4		28764

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	1.5	1.55	95.4		0.293		6.6	2760

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	PDB ENTRY 1F7A	1.5	39.2	28726	1465	96.93	0.1652	0.1637	0.1744	0.1933	0.1993	RANDOM	18.4068

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]
-1.18			0.49		0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.843
r_dihedral_angle_4_deg	13.334
r_dihedral_angle_3_deg	11.672
r_dihedral_angle_1_deg	6.039
r_angle_other_deg	1.979
r_angle_refined_deg	1.493
r_chiral_restr	0.094
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1498
Nucleic Acid Atoms
Solvent Atoms	168
Heterogen Atoms	65

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BioCARS-developed	data collection
HKL-2000	data reduction
AMoRE	phasing