8XO6 | pdb_00008xo6

Crystal structure of measles virus fusion inhibitor MEK35GE complexed with F protein HR1 (HR1-42) (P21212 space group)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	200 mM Zn Acetate, 18% (w/v) PEG 8000, 100 mM MES (pH 6.5)

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.049	α = 90
b = 59.768	β = 90
c = 63.674	γ = 90

Symmetry
Space Group	P 21 21 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 PILATUS3 6M		2019-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.000000	SPring-8	BL45XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	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	1.457	50	98.6	0.098	0.997	16.92	13.14		37542

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.457	1.55	96.6		0.875	0.968	2.83

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.457	43.604	37537	1855	98.584	0.178	0.1764	0.1772	0.2081	0.2087	22.054

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]
1.641			-0.395		-1.246

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.953
r_dihedral_angle_4_deg	20.82
r_dihedral_angle_3_deg	14.548
r_lrange_it	6.388
r_lrange_other	6.387
r_scangle_it	5.264
r_scangle_other	5.262
r_dihedral_angle_1_deg	3.756
r_scbond_it	3.523
r_scbond_other	3.522
r_mcangle_it	2.809
r_mcangle_other	2.804
r_mcbond_it	1.94
r_mcbond_other	1.921
r_angle_refined_deg	1.695
r_angle_other_deg	1.545
r_symmetry_nbd_refined	0.287
r_nbd_refined	0.219
r_symmetry_xyhbond_nbd_refined	0.197
r_metal_ion_refined	0.174
r_nbd_other	0.173
r_xyhbond_nbd_refined	0.172
r_nbtor_refined	0.168
r_symmetry_nbd_other	0.162
r_symmetry_metal_ion_refined	0.089
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1792
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	26

Software

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