3SAC | pdb_00003sac

Crystal structure of wild-type HIV-1 protease in complex with AF80

X-RAY DIFFRACTION

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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
2.1	41.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.88	α = 90
b = 58.001	β = 90
c = 61.567	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 315		2010-01-20		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A		NSLS	X29A

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	99.1	0.046	14.8	5.5		29473

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	99.3		0.352		5.3	2879

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	39.22	29319	1483	98.71	0.1819	0.1808	0.1905	0.2038	0.2131	RANDOM	21.501

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]
-0.91			-0.02		0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.176
r_dihedral_angle_4_deg	13.326
r_dihedral_angle_3_deg	10.617
r_dihedral_angle_1_deg	5.758
r_scangle_it	2.175
r_angle_refined_deg	1.445
r_scbond_it	1.319
r_mcangle_it	0.857
r_angle_other_deg	0.756
r_mcbond_it	0.471
r_mcbond_other	0.111
r_chiral_restr	0.072
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1502
Nucleic Acid Atoms
Solvent Atoms	148
Heterogen Atoms	49

Software

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