3NR6 | pdb_00003nr6

Crystal structure of xenotropic murine leukemia virus-related virus (XMRV) protease

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		ASSEMBLY OF RETROVIRAL PROTEASES

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	PROTEIN CONCENTRATION: 10 MG/ML PRECIPITANT: 0.06 M KH2PO4, 1.34 M NA2HPO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.915	α = 90
b = 63.915	β = 90
c = 106.509	γ = 90

Symmetry
Space Group	P 4 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	CCD	MARMOSAIC 300 mm CCD	MIRRORS	2010-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.97	50	98.5	0.044	0.044	32.1	4.3	16141	16141	-1.74	-3	37.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.97	2	82.1		0.257	0.257	3.23	2.9	667

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	ASSEMBLY OF RETROVIRAL PROTEASES	1.97	20	15336	815	98.46	0.19737	0.19737	0.19568	0.21	0.23322	0.25	RANDOM	47.871

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]
0.48			0.48		-0.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.578
r_dihedral_angle_3_deg	17.844
r_dihedral_angle_4_deg	15.2
r_dihedral_angle_1_deg	7.603
r_scangle_it	5.066
r_mcangle_it	4.062
r_scbond_it	3.676
r_mcbond_it	2.739
r_angle_refined_deg	1.837
r_chiral_restr	0.145
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1791
Nucleic Acid Atoms
Solvent Atoms	66
Heterogen Atoms	6

Software

Software
Software Name	Purpose
MAR345	data collection
PHASER	phasing
Rosetta	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
Rosetta	phasing