8XO5 | pdb_00008xo5

Crystal structure of measles virus fusion inhibitor MEK28 complexed with F protein HR1 (HR1-40) (H3 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	293	200 mM Ammonium Acetate, 40% (v/v) MPD, 100 mM MES buffer (pH 6.0)

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.8	α = 90
b = 51.8	β = 90
c = 58.662	γ = 120

Symmetry
Space Group	H 3

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	1.205	50	99.8	0.092	0.993	10.98	5.04		18126

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	1.205	1.28	99.1		0.541	0.969	2.72	4.87

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	1.205	35.635	18108	906	99.719	0.197	0.1952	0.205	0.231	0.2359	26.999

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]
0.718	0.359		0.718		-2.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.692
r_dihedral_angle_3_deg	15.57
r_dihedral_angle_4_deg	12.154
r_lrange_it	6.732
r_lrange_other	6.728
r_scangle_it	5.366
r_scangle_other	5.361
r_scbond_it	3.509
r_scbond_other	3.504
r_mcangle_other	2.974
r_mcangle_it	2.958
r_dihedral_angle_1_deg	2.839
r_mcbond_it	2.003
r_mcbond_other	1.968
r_angle_refined_deg	1.734
r_angle_other_deg	1.44
r_symmetry_nbd_refined	0.247
r_nbd_refined	0.217
r_nbd_other	0.201
r_symmetry_xyhbond_nbd_refined	0.188
r_xyhbond_nbd_refined	0.172
r_nbtor_refined	0.161
r_symmetry_nbd_other	0.148
r_symmetry_nbtor_other	0.089
r_chiral_restr	0.088
r_bond_refined_d	0.012
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	547
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	8

Software

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