1SP5 | pdb_00001sp5

Crystal structure of HIV-1 protease complexed with a product of autoproteolysis

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1A30	PDB ENTRY 1A30

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	279	sodium chloride 0.8-0.9M, sodium citrate 50mM, DMSO 5%, sodium acetate 5mM, EDTA 0.5mM, DTT 0.25mM, Boc-Phe-psi[(S)-CH(OH)CH2NH]Phe-Ile-Phe-NH2 270mM, protein 3mg/ml in drop, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K

Crystal Properties
Matthews coefficient	Solvent content
2.37	47.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.765	α = 90
b = 86.284	β = 90
c = 45.834	γ = 90

Symmetry
Space Group	P 21 21 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	IMAGE PLATE	MARRESEARCH		2000-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.0	ELETTRA	5.2R

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	1.801	25	96.7	0.049	0.049	30.8	4.3	21152	21152			14

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)
	1.8	1.83	92.9		0.232	0.232	7	3.8	988

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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1A30	1.8	19.1	21129	21129	1023	96.7	0.178	0.178	0.177	0.17	0.211	0.17	RANDOM	15.9

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]

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	26.2
c_scangle_it	4.57
c_scbond_it	3.03
c_mcangle_it	2.33
c_angle_deg	1.6
c_mcbond_it	1.55
c_improper_angle_d	0.92
c_bond_d	0.013
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1567
Nucleic Acid Atoms
Solvent Atoms	135
Heterogen Atoms	19

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing