8XO4 | pdb_00008xo4

Crystal structure of measles virus fusion inhibitor M1EK complexed with F protein HR1 (HR1-42) (P21 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	5.5	293	200 mM MgCl2, 24% (w/v) PEG 3350, 100 mM BIS-TRIS (pH 5.5)

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.843	α = 90
b = 35.58	β = 93.982
c = 237.649	γ = 90

Symmetry
Space Group	P 1 21 1

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		2019-07-18	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	2.362	50	99.5	0.057	0.999	18.68	6.59		39067

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	2.362	2.5	97.9		0.528	0.965	2.82	6.46

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	2.362	49.105	39054	1953	99.518	0.22	0.2153	0.2229	0.3006	0.3014	65.125

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]
3.605		-0.173	4.568		-8.071

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.991
r_dihedral_angle_3_deg	19.315
r_dihedral_angle_4_deg	18.134
r_lrange_it	11.824
r_lrange_other	11.824
r_scangle_it	9.759
r_scangle_other	9.758
r_mcangle_it	7.691
r_mcangle_other	7.686
r_scbond_it	6.412
r_scbond_other	6.411
r_mcbond_it	5.492
r_mcbond_other	5.48
r_dihedral_angle_1_deg	5.175
r_angle_refined_deg	1.535
r_angle_other_deg	1.253
r_symmetry_nbd_refined	0.244
r_nbd_refined	0.222
r_symmetry_xyhbond_nbd_refined	0.211
r_nbd_other	0.2
r_symmetry_nbd_other	0.171
r_xyhbond_nbd_refined	0.158
r_nbtor_refined	0.145
r_symmetry_nbtor_other	0.1
r_chiral_restr	0.072
r_symmetry_xyhbond_nbd_other	0.02
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7500
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms

Software

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