3GI6 | pdb_00003gi6

Crystal structure of protease inhibitor, AD78 in complex with wild type HIV-1 protease

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.2	298	126 mM sodium phosphate pH 6.2, 63 mM sodium citrate, 24-29% ammonium sulphate, vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.803	α = 90
b = 58.021	β = 90
c = 61.671	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	200	IMAGE PLATE	RIGAKU RAXIS IV			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	1.84	50	95.7	0.058		7		15595

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	1.84	1.92	89.1		0.358		6.4	1414

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	1.84	24	15562	789	95.48	0.166	0.164	0.18	0.196	0.21	RANDOM	24.683

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]
-0.89			0.13		0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.012
r_dihedral_angle_4_deg	17.149
r_dihedral_angle_3_deg	10.575
r_dihedral_angle_1_deg	5.722
r_scangle_it	1.484
r_angle_refined_deg	1.283
r_scbond_it	0.96
r_angle_other_deg	0.694
r_mcangle_it	0.681
r_mcbond_it	0.48
r_nbd_refined	0.183
r_nbd_other	0.173
r_symmetry_vdw_other	0.169
r_nbtor_refined	0.165
r_symmetry_hbond_refined	0.158
r_xyhbond_nbd_refined	0.136
r_symmetry_vdw_refined	0.124
r_mcbond_other	0.1
r_nbtor_other	0.079
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1482
Nucleic Acid Atoms
Solvent Atoms	163
Heterogen Atoms	61

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
AMoRE	phasing