3O99

Crystal Structure of wild-type HIV-1 Protease in complex with kd13

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		6.2	295	126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 24-29% Ammonium Sulfate, hanging drop, vapor diffusion, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.774	α = 90
b = 57.885	β = 90
c = 61.752	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	YALE MIRRORS	2008-08-26		SINGLE WAVELENGTH

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

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	1.95	50	99.9	0.09	8.3	6.7		13796

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	1.95	2.02	99.8		0.414		5.7

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1F7A	1.95	39.22	13067	687	99.81	0.17909	0.17673	0.2244	RANDOM	22.71

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			0.02		0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.925
r_dihedral_angle_4_deg	17.232
r_dihedral_angle_3_deg	11.934
r_dihedral_angle_1_deg	6.296
r_scangle_it	1.89
r_angle_refined_deg	1.431
r_scbond_it	1.293
r_angle_other_deg	0.84
r_mcangle_it	0.718
r_mcbond_it	0.531
r_nbd_refined	0.198
r_nbd_other	0.196
r_symmetry_hbond_refined	0.188
r_nbtor_refined	0.17
r_symmetry_vdw_refined	0.167
r_symmetry_vdw_other	0.145
r_xyhbond_nbd_refined	0.143
r_mcbond_other	0.141
r_nbtor_other	0.086
r_chiral_restr	0.085
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
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	1486
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	53

Software

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