8XO8 | pdb_00008xo8

Crystal structure of measles virus fusion inhibitor MEK35GT complexed with F protein HR1 (HR1-42) (P21 space group)

X-RAY DIFFRACTION

---

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	7.5	293	10% (v/v) 2-propanol, 20% (w/v) PEG 4000, 100 mM HEPES (pH 7.5)

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.747	α = 90
b = 53.577	β = 94.957
c = 109.051	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 EIGER X 16M		2020-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.999990	SPring-8	BL41XU

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	1.846	50	99.3	0.051	0.999	17.13	3.45		36255

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	1.846	1.96	98.9		0.482	0.865	2.78	3.53

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	1.846	48.005	36252	1692	99.312	0.183	0.18	0.1886	0.2396	0.2482	29.816

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]
0.662		-1.807	0.136		-0.477

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.698
r_dihedral_angle_4_deg	16.319
r_dihedral_angle_3_deg	16.127
r_lrange_it	6.715
r_lrange_other	6.591
r_scangle_it	4.952
r_scangle_other	4.951
r_dihedral_angle_1_deg	4.251
r_mcangle_it	3.257
r_mcangle_other	3.252
r_scbond_it	3.09
r_scbond_other	3.09
r_mcbond_it	2.316
r_mcbond_other	2.311
r_angle_refined_deg	1.402
r_angle_other_deg	1.351
r_symmetry_nbd_refined	0.231
r_nbd_other	0.208
r_nbd_refined	0.207
r_symmetry_xyhbond_nbd_refined	0.181
r_xyhbond_nbd_refined	0.17
r_symmetry_nbd_other	0.165
r_nbtor_refined	0.144
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.071
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	3626
Nucleic Acid Atoms
Solvent Atoms	408
Heterogen Atoms

Software

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