8AXG | pdb_00008axg

Crystal structure of Fusobacterium nucleatum fusolisin protease

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		297	100mM Bis-Tris pH 6.5 and 20% PEG MME5000

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.475	α = 90
b = 115.475	β = 90
c = 196.786	γ = 90

Symmetry
Space Group	P 41

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 EIGER2 XE 16M		2020-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.04	75.42	91.6	0.976	8.4	12.9		149218

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.04	2.07			0.193

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	assembly	2.04	74.893	148870	7308	91.276	0.179	0.1771	0.18	0.2158	0.22	41.11

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]
-1.14			-1.14		2.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.958
r_dihedral_angle_4_deg	16.608
r_dihedral_angle_3_deg	13.414
r_lrange_it	7.96
r_dihedral_angle_1_deg	5.899
r_scangle_it	5.756
r_scbond_it	4.185
r_mcangle_it	4.173
r_mcbond_it	2.942
r_angle_refined_deg	1.375
r_nbtor_refined	0.308
r_symmetry_nbd_refined	0.251
r_nbd_refined	0.198
r_symmetry_xyhbond_nbd_refined	0.164
r_xyhbond_nbd_refined	0.125
r_chiral_restr	0.091
r_ncsr_local_group_1	0.078
r_ncsr_local_group_3	0.077
r_ncsr_local_group_2	0.075
r_ncsr_local_group_5	0.074
r_ncsr_local_group_4	0.065
r_ncsr_local_group_6	0.062
r_gen_planes_refined	0.007
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17055
Nucleic Acid Atoms
Solvent Atoms	1705
Heterogen Atoms	584

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
pointless	data scaling
Aimless	data scaling
PHASER	phasing
PARROT	phasing