7D21

Crystal structure of Ixodes scapularis glutaminyl cyclase with two Zn ions bound to the active site

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4MHN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293.15	10%(w/v) PEG8000, 8%(v/v) ethylene glycol, 0.1 M HEPES pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.646	α = 90
b = 70.932	β = 90
c = 80.556	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX300HE		2017-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL15A1	1.0	NSRRC	BL15A1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.97	30	99.9	0.09	31.1	5.6		23206

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.97	2.04	100		0.855	2.6	5.6

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	4MHN	1.97	27.84	21965	1189	99.59	0.1908	0.1891	0.2224	RANDOM	41.856

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]
0.89			-0.09		-0.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.992
r_dihedral_angle_4_deg	17.151
r_dihedral_angle_3_deg	15.392
r_dihedral_angle_1_deg	5.671
r_angle_refined_deg	1.282
r_angle_other_deg	0.988
r_chiral_restr	0.072
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.992
r_dihedral_angle_4_deg	17.151
r_dihedral_angle_3_deg	15.392
r_dihedral_angle_1_deg	5.671
r_angle_refined_deg	1.282
r_angle_other_deg	0.988
r_chiral_restr	0.072
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2688
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

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 R01GM157729.