8XO2 | pdb_00008xo2

Crystal structure of measles virus fusion inhibitor M1 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	8.5	293	200 mM MgCl2, 27% (w/v) PEG 3350, 100 mM Tris (pH 8.5)

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.038	α = 90
b = 54.78	β = 90
c = 64.623	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		2019-07-18	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	1.306	50	99.9	0.061	0.998	17.71	6.43		47235

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	1.306	1.38	99.7		0.431	0.94	3.88	6.5

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	1.306	41.803	47221	2361	99.928	0.181	0.1794	0.18	0.2046	0.2062	18.286

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]
0.203			0.632		-0.835

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.548
r_dihedral_angle_4_deg	15.514
r_dihedral_angle_3_deg	13.011
r_lrange_it	6.459
r_lrange_other	6.187
r_scangle_it	4.178
r_scangle_other	4.177
r_dihedral_angle_1_deg	3.703
r_scbond_it	2.853
r_scbond_other	2.852
r_mcangle_it	2.261
r_mcangle_other	2.261
r_angle_refined_deg	1.756
r_angle_other_deg	1.625
r_mcbond_it	1.494
r_mcbond_other	1.494
r_symmetry_nbd_refined	0.267
r_nbd_refined	0.231
r_nbd_other	0.22
r_symmetry_xyhbond_nbd_refined	0.203
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.164
r_symmetry_nbd_other	0.16
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.082
r_metal_ion_refined	0.036
r_bond_refined_d	0.013
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	1742
Nucleic Acid Atoms
Solvent Atoms	342
Heterogen Atoms	4

Software

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