4Q1Y | pdb_00004q1y

Mutations Outside the Active Site of HIV-1 Protease Alter Enzyme Structure and Dynamic Ensemble of the Active Site to Confer Drug Resistance

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	295	126mM Phosphate buffer, 63mM Sodium Citrate, 24-29% Ammonium Sulfate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.813	α = 90
b = 58.225	β = 90
c = 61.824	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	CCD	ADSC QUANTUM 315	Bent conical Si-mirror (Rh coated)	2008-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9002	APS	14-BM-C

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	1.5	39.25	98.8	0.048	16.8	6.5	29633	29633	3	3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.55	96.7			5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.5	39.25	29773	28079	1497	98.72	0.1838	0.18253	0.18	0.20737	0.21	RANDOM	25.341

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]
-1.22			1.26		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.325
r_dihedral_angle_3_deg	11.65
r_dihedral_angle_4_deg	10.289
r_dihedral_angle_1_deg	6.237
r_scangle_it	2.464
r_scbond_it	1.768
r_angle_refined_deg	1.497
r_mcangle_it	1.116
r_angle_other_deg	0.876
r_mcbond_it	0.817
r_nbd_other	0.204
r_nbd_refined	0.199
r_mcbond_other	0.199
r_symmetry_hbond_refined	0.185
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.144
r_symmetry_vdw_other	0.131
r_chiral_restr	0.1
r_symmetry_vdw_refined	0.095
r_nbtor_other	0.088
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1506
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	65

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-3000	data reduction
HKL-3000	data scaling
AMoRE	phasing