3IA9 | pdb_00003ia9

Crystal structure of a chemically synthesized [D25N]HIV-1 protease molecule complexed with MVT-101 reduced isostere inhibitor

X-RAY DIFFRACTION

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Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.09	α = 90
b = 57.697	β = 90
c = 61.832	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		2008-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.00000	APS	21-ID-D

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	1.3	50	99.8	0.055	32.97	5.9		45790

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	1.3	1.35	98.6		0.375	3.36	3.1	4507

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.3	20	43280	2303	99.44	0.1795	0.17801	0.1872	0.20786	0.2153	RANDOM	12.869

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]
-0.19			0.06		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.077
r_dihedral_angle_4_deg	17.327
r_dihedral_angle_3_deg	12.172
r_dihedral_angle_1_deg	6.668
r_scangle_it	4.826
r_sphericity_bonded	4.623
r_scbond_it	4.069
r_rigid_bond_restr	3.351
r_mcangle_it	2.464
r_mcbond_it	1.783
r_angle_refined_deg	1.697
r_mcbond_other	1.105
r_angle_other_deg	0.935
r_nbd_other	0.206
r_nbd_refined	0.198
r_symmetry_vdw_other	0.183
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.139
r_symmetry_hbond_refined	0.121
r_chiral_restr	0.104
r_symmetry_vdw_refined	0.094
r_nbtor_other	0.089
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_free

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1518
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	64

Software

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