1ZY7 | pdb_00001zy7

Crystal structure of the catalytic domain of an adenosine deaminase that acts on RNA (hADAR2) bound to inositol hexakisphosphate (IHP)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.8	293	Bis-Tris, ammonium sulfate, PEG 3350, glycerol, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.3	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.205	α = 90
b = 121.192	β = 90
c = 127.331	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	IMAGE PLATE	RIGAKU RAXIS IV		2004-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.7	20	92.3			89796	82849		-2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.7	1.76	62.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MIR	1.7	20	89813	82731	4219	92.27	0.17461	0.17461	0.173	0.17	0.206	0.18	5%	19.71

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]
0.46			-0.27		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.142
r_dihedral_angle_4_deg	18.876
r_dihedral_angle_3_deg	13.553
r_dihedral_angle_1_deg	5.74
r_scangle_it	3.651
r_scbond_it	2.409
r_mcangle_it	1.573
r_angle_refined_deg	1.48
r_mcbond_it	0.943
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.142
r_dihedral_angle_4_deg	18.876
r_dihedral_angle_3_deg	13.553
r_dihedral_angle_1_deg	5.74
r_scangle_it	3.651
r_scbond_it	2.409
r_mcangle_it	1.573
r_angle_refined_deg	1.48
r_mcbond_it	0.943
r_nbtor_refined	0.304
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.194
r_xyhbond_nbd_refined	0.155
r_symmetry_hbond_refined	0.146
r_chiral_restr	0.098
r_metal_ion_refined	0.041
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5803
Nucleic Acid Atoms
Solvent Atoms	669
Heterogen Atoms	79

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

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.