2QI0 | pdb_00002qi0

Crystal structure of protease inhibitor, MIT-1-KK80 in complex with wild type HIV-1 protease

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	VAPOR DIFFUSION, HANGING DROP	6.2	298	126 mM Sodium Phosphate, 63 mM sodium citrate, 24-29% ammonium sulphate , pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.975	α = 90
b = 58.242	β = 90
c = 61.701	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	osmic mirrors	2006-02-23	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)	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	2.1	50	99	0.051	5.1	10.7	6.9		11126

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 (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	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1F7A	2.1	42.37	10563	530	99.03	0.17307	0.17307	0.17034	0.18	0.2302	0.24	RANDOM	30.983

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]
-0.71			0.17		0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.691
r_dihedral_angle_3_deg	13.17
r_dihedral_angle_4_deg	13.139
r_dihedral_angle_1_deg	6.855
r_scangle_it	2.534
r_scbond_it	1.626
r_angle_refined_deg	1.267
r_mcangle_it	1.018
r_mcbond_it	0.718
r_angle_other_deg	0.65
r_nbd_other	0.192
r_nbd_refined	0.182
r_mcbond_other	0.178
r_symmetry_vdw_other	0.174
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.153
r_symmetry_hbond_refined	0.144
r_symmetry_vdw_refined	0.127
r_nbtor_other	0.083
r_chiral_restr	0.079
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1490
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing