8XO3 | pdb_00008xo3

Crystal structure of measles virus fusion inhibitor M1 complexed with F protein HR1 (HR1-47) (P321 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 Ca Acetate, 15% (w/v) PEG 3350, 100 mM BIS-TRIS (pH 6.5)

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.899	α = 90
b = 32.899	β = 90
c = 124.596	γ = 120

Symmetry
Space Group	P 3 2 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	1.104	50	99.1	0.094	0.996	13.02	8.66		32332

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	1.104	1.17	94.3		0.619	0.969	2	5.25

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	1.104	41.532	32301	1615	98.983	0.214	0.2127	0.2225	0.2353	0.2481	23.384

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]
0.754	0.377		0.754		-2.445

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.238
r_dihedral_angle_4_deg	12.491
r_dihedral_angle_3_deg	12.426
r_lrange_it	5.8
r_lrange_other	5.391
r_scangle_other	4.415
r_scangle_it	4.409
r_dihedral_angle_1_deg	3.756
r_scbond_it	2.828
r_scbond_other	2.798
r_mcangle_it	2.448
r_mcangle_other	2.432
r_mcbond_it	1.874
r_mcbond_other	1.853
r_angle_refined_deg	1.773
r_angle_other_deg	1.633
r_metal_ion_refined	0.231
r_nbd_refined	0.23
r_symmetry_xyhbond_nbd_refined	0.208
r_nbd_other	0.177
r_xyhbond_nbd_refined	0.176
r_nbtor_refined	0.168
r_symmetry_nbd_other	0.158
r_symmetry_nbd_refined	0.131
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.014
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	636
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	1

Software

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