7ZAS | pdb_00007zas

Crystal structure of cleaved Iripin-4 serpin from tick Ixodes ricinus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		MrBUMP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277	0.2 M Ammonium acetate, 0.1 M BIS-Tris, 25 % w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.699	α = 90
b = 138.414	β = 107.7
c = 80.217	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 PILATUS 6M		2021-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

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	46.42	99.3	0.167	0.997	9.1	6.92		91690			33.66

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	2.12	98.6		0.773

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	MrBUMP	2	46.42	89590	2100	99.38	0.1884	0.187	0.1927	0.2496	0.2527	RANDOM	26.222

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]
-1.69		-0.44	0.03		1.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.93
r_dihedral_angle_3_deg	12.356
r_dihedral_angle_4_deg	12.086
r_dihedral_angle_1_deg	7.914
r_angle_refined_deg	1.442
r_angle_other_deg	1.262
r_chiral_restr	0.061
r_bond_refined_d	0.007
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	11786
Nucleic Acid Atoms
Solvent Atoms	1323
Heterogen Atoms	4

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction