6OYD

X-ray crystal structure of wild type HIV-1 protease in complex with GRL-004

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5TYR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	0.2 M Sodium chloride, 0.1 M MES (pH 6.5), 10%(w/v) PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.825	α = 90
b = 62.825	β = 90
c = 82.28	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2016-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.46	54.41	99.63	14.1	18.6		17208

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	1.46	1.512

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	5TYR	1.46	54.41	16345	860	99.64	0.22009	0.21819	0.25721	RANDOM	23.611

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]
0.05	0.02		0.05		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.707
r_dihedral_angle_4_deg	24.206
r_dihedral_angle_3_deg	13.384
r_dihedral_angle_1_deg	8.104
r_long_range_B_other	5.926
r_long_range_B_refined	5.923
r_scangle_other	4.723
r_scbond_it	3.136
r_scbond_other	3.132
r_mcangle_it	3.091
r_mcangle_other	3.091
r_mcbond_it	2.294
r_mcbond_other	2.289
r_angle_refined_deg	2.003
r_angle_other_deg	1.62
r_chiral_restr	0.095
r_bond_refined_d	0.015
r_gen_planes_refined	0.015
r_gen_planes_other	0.009
r_bond_other_d	0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	760
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms	47

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing