8IUI | pdb_00008iui

Crystal structure of silkworm fibroinase complexed with E-64

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YCC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	30% w/v Polyethylene glycol monomethyl ether 2,000, 0.1 M Potassium thiocyanate

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.18	α = 90
b = 64.69	β = 97.641
c = 92.91	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 PILATUS3 6M		2019-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.979	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.56	92.09	99.6	0.131	0.143	0.055	8.1	6.7		58638

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.56	1.6	98.8		0.392	0.425	0.164		6.8

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	1.56	92.085	58624	2863	99.58	0.233	0.2313	0.24	0.2693	0.27	15.376

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]
-1.645		0.077	-0.904		2.441

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.002
r_dihedral_angle_4_deg	15.972
r_dihedral_angle_3_deg	13.245
r_dihedral_angle_1_deg	7.227
r_lrange_it	3.741
r_lrange_other	3.722
r_scangle_it	2.953
r_scangle_other	2.952
r_scbond_it	1.935
r_scbond_other	1.935
r_mcangle_other	1.869
r_mcangle_it	1.868
r_angle_refined_deg	1.601
r_angle_other_deg	1.441
r_mcbond_it	1.212
r_mcbond_other	1.204
r_nbd_refined	0.216
r_symmetry_nbd_other	0.184
r_symmetry_xyhbond_nbd_refined	0.172
r_nbtor_refined	0.171
r_nbd_other	0.17
r_xyhbond_nbd_refined	0.146
r_symmetry_nbd_refined	0.142
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3360
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing