8R28 | pdb_00008r28

Crystal structure of Amacstatin-1, 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
experimental model	PDB	6ZTK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	0.2 M ammonium phosphate, 0.1 M Tris-HCl pH 8.5, 50% (v/v) MPD

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.411	α = 90
b = 98.411	β = 90
c = 27.579	γ = 120

Symmetry
Space Group	P 65

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 300K		2020-01-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.541870

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.807	42.61	92.1	0.068	0.998	80.7	4.5		13304

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.807	1.84	21.5		0.129	0.177	0.965		1.3

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	1.807	28.425	13190	686	91.737	0.163	0.161	0.1623	0.2023	0.2039	21.061

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]
0.769	0.384		0.769		-2.493

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.724
r_dihedral_angle_3_deg	14.428
r_dihedral_angle_2_deg	9.996
r_lrange_it	6.936
r_dihedral_angle_1_deg	6.826
r_lrange_other	6.718
r_scangle_it	5.18
r_scangle_other	5.092
r_scbond_it	3.469
r_scbond_other	3.404
r_mcangle_other	3.361
r_mcangle_it	3.331
r_mcbond_it	2.314
r_mcbond_other	2.185
r_angle_refined_deg	1.51
r_angle_other_deg	0.508
r_symmetry_nbd_other	0.205
r_nbd_refined	0.194
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.154
r_symmetry_nbd_refined	0.146
r_nbd_other	0.136
r_symmetry_xyhbond_nbd_refined	0.122
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.07
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	817
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	5

Software

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