8R29 | pdb_00008r29

Crystal structure of domain swapped dimer of Amacstatin-2, a cystatin from the hard tick Amblyomma maculatum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	G3MQC0	N-terminus truncated to Gly29

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	0.1 M bicine-Tris-HCl pH 8.5, 12.5% w/v PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 0.3 M diethyleneglycol, 0.3 M triethyleneglycol, 0.3 M tetraethyleneglycol, and 0.3 M pentaethyleneglycol

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.172	α = 90
b = 49.172	β = 90
c = 86.458	γ = 90

Symmetry
Space Group	P 43

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		2019-10-04	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)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.146	49.172	92.28	0.116	0.1256	0.04719	0.997	10.34	6.8		10697			44.96

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.146	2.227	61.42		5.08	5.828	2.766	0.396		4.1

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.146	49.172	10385	520	92.155	0.228	0.2257	0.2175	0.2746	0.266	Random selection	49.134

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]
0.617			0.617		-1.235

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.874
r_dihedral_angle_6_deg	14.978
r_dihedral_angle_2_deg	12.698
r_lrange_it	10.269
r_lrange_other	10.266
r_scangle_it	8.3
r_scangle_other	8.296
r_dihedral_angle_1_deg	7.781
r_mcangle_it	7.429
r_mcangle_other	7.426
r_scbond_it	5.687
r_scbond_other	5.683
r_mcbond_it	5.205
r_mcbond_other	5.202
r_angle_refined_deg	1.62
r_angle_other_deg	0.535
r_xyhbond_nbd_refined	0.321
r_nbd_refined	0.223
r_symmetry_nbd_other	0.218
r_nbd_other	0.197
r_nbtor_refined	0.183
r_ncsr_local_group_1	0.147
r_symmetry_nbtor_other	0.091
r_chiral_restr	0.07
r_symmetry_nbd_refined	0.048
r_symmetry_xyhbond_nbd_refined	0.031
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1613
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms

Software

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