7AHP

Crystal structure of Ixodes ricinus serpin - Iripin-3

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NDA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293.15	potassium thiocyanate, sodium cacodylate, PGA

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.94	α = 90
b = 132.94	β = 90
c = 88.89	γ = 120

Symmetry
Space Group	P 62 2 2

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		2019-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

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	1.95	48.32	99.9	0.998	0.1345	1.573		34278

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	1.95	2.07			0.826

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3nda	1.95	48.32	32559	1714	99.86	0.1931	0.1916	0.2228	RANDOM	24.264

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]
0.31	0.16		0.31		-1.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.443
r_dihedral_angle_4_deg	14.407
r_dihedral_angle_3_deg	11.268
r_dihedral_angle_1_deg	6.102
r_angle_other_deg	2.307
r_angle_refined_deg	1.709
r_chiral_restr	0.122
r_bond_other_d	0.035
r_bond_refined_d	0.015
r_gen_planes_other	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.443
r_dihedral_angle_4_deg	14.407
r_dihedral_angle_3_deg	11.268
r_dihedral_angle_1_deg	6.102
r_angle_other_deg	2.307
r_angle_refined_deg	1.709
r_chiral_restr	0.122
r_bond_other_d	0.035
r_bond_refined_d	0.015
r_gen_planes_other	0.006
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2874
Nucleic Acid Atoms
Solvent Atoms	251
Heterogen Atoms	24

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.