3EM6 | pdb_00003em6

Crystal structure of I50L/A71V mutant of hiv-1 protease in complex with inhibitor darunavir

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F7A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	300	pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.14	α = 90
b = 57.891	β = 90
c = 61.364	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	Yale Mirrors	2004-03-28	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	2.1	50	96.6	0.092	11.443	3.2		10762

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	2.1	2.18	95.6		0.461			1027

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1F7A	2.1	42.26	10740	507	96.79	0.188	0.186	0.2	0.24	0.25	RANDOM	6.32

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]
-0.4			-0.46		0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.145
r_dihedral_angle_4_deg	14.465
r_dihedral_angle_3_deg	13.456
r_dihedral_angle_1_deg	6.315
r_angle_refined_deg	1.151
r_scangle_it	1.056
r_angle_other_deg	0.825
r_scbond_it	0.722
r_mcangle_it	0.485
r_mcbond_it	0.439
r_symmetry_vdw_other	0.197
r_nbd_other	0.182
r_symmetry_hbond_refined	0.18
r_nbd_refined	0.178
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.165
r_symmetry_vdw_refined	0.151
r_nbtor_other	0.082
r_chiral_restr	0.067
r_mcbond_other	0.062
r_gen_planes_other	0.007
r_gen_planes_refined	0.006
r_bond_refined_d	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1458
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms	75

Software

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