8XNE | pdb_00008xne

Crystal structure of measles virus fusion inhibitor M1 complexed with F protein HR1 (HR1-42) (H32 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 MgCl2, 30% (w/v) PEG 3350, 100 mM MES (pH 6.5)

Crystal Properties
Matthews coefficient	Solvent content
1.79	31.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 28.506	α = 90
b = 28.506	β = 90
c = 387.637	γ = 120

Symmetry
Space Group	H 3 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		2019-07-18	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	1.155	50	99.6	0.096	0.998	15.71	8.72		22473

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	1.155	1.22	98.3		0.446	0.969	5.12	7.94

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	1.155	24.601	22463	1124	99.742	0.161	0.1597	0.1604	0.1871	0.1891	11.466

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]
0.119	0.06		0.119		-0.386

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.892
r_dihedral_angle_3_deg	12.412
r_dihedral_angle_4_deg	7.462
r_lrange_it	4.694
r_lrange_other	4.247
r_dihedral_angle_1_deg	3.391
r_scangle_it	3.059
r_scangle_other	3.056
r_scbond_it	2.15
r_scbond_other	2.15
r_angle_refined_deg	1.813
r_angle_other_deg	1.684
r_mcangle_it	1.414
r_mcangle_other	1.396
r_mcbond_it	1.039
r_mcbond_other	1.001
r_symmetry_nbd_refined	0.251
r_nbd_refined	0.224
r_nbd_other	0.224
r_symmetry_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.174
r_symmetry_nbd_other	0.154
r_xyhbond_nbd_refined	0.147
r_xyhbond_nbd_other	0.117
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	595
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	2

Software

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