2PSV | pdb_00002psv

Crystal Structure of wild type HIV-1 protease in complex with CARB-KB45

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

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.692	α = 90
b = 57.593	β = 90
c = 61.836	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		IMAGE PLATE	RIGAKU RAXIS IV	osmic mirrors	2005-12-21	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	1.7	50	94.6	0.045	15.1	5.9		19450

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	1.75	42.14	17590	937	98.4	0.16737	0.16737	0.16527	0.17	0.2076	0.22	RANDOM	17.847

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]
-0.55					0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.288
r_dihedral_angle_4_deg	15.583
r_dihedral_angle_3_deg	11.117
r_dihedral_angle_1_deg	6.317
r_scangle_it	1.575
r_angle_refined_deg	1.266
r_scbond_it	1.022
r_angle_other_deg	0.842
r_mcangle_it	0.684
r_mcbond_it	0.489
r_nbd_refined	0.184
r_symmetry_vdw_other	0.179
r_symmetry_vdw_refined	0.173
r_nbd_other	0.17
r_nbtor_refined	0.164
r_symmetry_hbond_refined	0.13
r_xyhbond_nbd_refined	0.105
r_mcbond_other	0.098
r_nbtor_other	0.077
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1488
Nucleic Acid Atoms
Solvent Atoms	195
Heterogen Atoms	52

Software

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