7D23 | pdb_00007d23

Crystal structure of Ixodes scapularis glutaminyl cyclase with one K ion 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
2.09	41.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.471	α = 90
b = 71.2	β = 90
c = 80.092	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	1.4	30	99.4	0.058	22.2	3.8		62791

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	1.4	1.45	99.9		0.51	1.9	3.7

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	4MHN	1.4	24	59549	3183	99.31	0.1611	0.1598	0.16	0.1863	0.19	RANDOM	17.568

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]
0.24			0.05		-0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.77
r_sphericity_free	21.207
r_dihedral_angle_4_deg	13.298
r_dihedral_angle_3_deg	12.388
r_sphericity_bonded	6.085
r_dihedral_angle_1_deg	5.152
r_rigid_bond_restr	1.69
r_angle_refined_deg	1.131
r_chiral_restr	0.077
r_bond_refined_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.77
r_sphericity_free	21.207
r_dihedral_angle_4_deg	13.298
r_dihedral_angle_3_deg	12.388
r_sphericity_bonded	6.085
r_dihedral_angle_1_deg	5.152
r_rigid_bond_restr	1.69
r_angle_refined_deg	1.131
r_chiral_restr	0.077
r_bond_refined_d	0.005
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2665
Nucleic Acid Atoms
Solvent Atoms	393
Heterogen Atoms	10

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.