8XO7 | pdb_00008xo7

Crystal structure of measles virus fusion inhibitor MEK35GE complexed with F protein HR1 (HR1-42) (P2 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, 25% (w/v) PEG 3350, 100 mM Tris (pH 8.5)

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.397	α = 90
b = 35.573	β = 91.262
c = 123.262	γ = 90

Symmetry
Space Group	P 1 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		2019-12-02	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	2.165	50	99	0.063	0.999	20.74	6.65		24545

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	2.165	2.3	96.6		0.514	0.951	3.77	6.34

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	2.165	48.605	24541	1246	98.956	0.207	0.2028	0.2092	0.2805	0.2842	49.786

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]
3.049		-1.308	2.488		-5.474

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.172
r_dihedral_angle_3_deg	17.892
r_dihedral_angle_4_deg	14.048
r_lrange_other	10.279
r_lrange_it	10.275
r_scangle_it	8.59
r_scangle_other	8.588
r_mcangle_it	6.351
r_mcangle_other	6.347
r_scbond_it	5.633
r_scbond_other	5.632
r_dihedral_angle_1_deg	4.981
r_mcbond_it	4.653
r_mcbond_other	4.651
r_angle_refined_deg	1.582
r_angle_other_deg	1.344
r_symmetry_nbd_refined	0.275
r_nbd_refined	0.213
r_nbd_other	0.2
r_xyhbond_nbd_refined	0.188
r_symmetry_nbd_other	0.173
r_symmetry_xyhbond_nbd_refined	0.158
r_nbtor_refined	0.152
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.073
r_symmetry_xyhbond_nbd_other	0.057
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3567
Nucleic Acid Atoms
Solvent Atoms	153
Heterogen Atoms

Software

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