2F3K | pdb_00002f3k

Substrate envelope and drug resistance: crystal structure of r01 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	5.5	298	0.126M Sodium Acetate; 0.063M Sodium citrate, 25-30% Ammonium sulphate, pH 5.5, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.873	α = 90
b = 58.167	β = 90
c = 61.653	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	IMAGE PLATE	RIGAKU RAXIS IV	Osmic Mirrors	2004-04-14	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	1.599	42.26	99.9	0.028	19.2	5.7	24814	24814

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)
	1.599	1.66	99.8		0.367

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 (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	1.599	19.53	24814	23503	1261	99.83	0.16489	0.16312	0.18	0.19667	0.21	RANDOM	17.07

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]
-0.62			0.11		0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.644
r_dihedral_angle_4_deg	17.428
r_dihedral_angle_3_deg	12.749
r_dihedral_angle_1_deg	7.331
r_angle_other_deg	3.532
r_scangle_it	2.589
r_scbond_it	1.76
r_angle_refined_deg	1.43
r_mcangle_it	1.169
r_mcbond_it	0.727
r_nbd_other	0.233
r_symmetry_hbond_refined	0.229
r_symmetry_vdw_other	0.227
r_nbd_refined	0.196
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.172
r_symmetry_vdw_refined	0.144
r_nbtor_other	0.111
r_chiral_restr	0.085
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_gen_planes_other	0.006
r_bond_other_d
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1827
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	130

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
AMoRE	phasing