9DP5 | pdb_00009dp5

Crystal Structure of Hydra Adenosine Deaminase Acting on RNA (ADAR) Deaminase Domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZY7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52940.2 M NaCl, 0.1 M Bis-Tris pH 6.5, 25% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.2945.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.4α = 83.109
b = 49.44β = 80.171
c = 83.04γ = 71.06
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2021-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.97946SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.9986595.20.0940.1110.9967.793.5247063-334.79
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)RedundancyNumber Unique Reflections (All)
122.0595.11.1231.3230.7371.233.54

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.99839.37647063254294.960.2130.21110.22220.24290.253253.135
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]
0.7321.7050.8850.4471.4710.216
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.562
r_dihedral_angle_6_deg15.514
r_dihedral_angle_2_deg11.577
r_lrange_other8.639
r_lrange_it8.638
r_dihedral_angle_1_deg6.762
r_mcangle_it5.027
r_mcangle_other5.027
r_scangle_it4.624
r_scangle_other4.623
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.562
r_dihedral_angle_6_deg15.514
r_dihedral_angle_2_deg11.577
r_lrange_other8.639
r_lrange_it8.638
r_dihedral_angle_1_deg6.762
r_mcangle_it5.027
r_mcangle_other5.027
r_scangle_it4.624
r_scangle_other4.623
r_mcbond_it2.867
r_mcbond_other2.865
r_scbond_it2.845
r_scbond_other2.845
r_angle_refined_deg1.672
r_angle_other_deg0.591
r_nbd_refined0.22
r_nbd_other0.22
r_symmetry_nbd_other0.214
r_nbtor_refined0.184
r_xyhbond_nbd_refined0.157
r_symmetry_nbd_refined0.144
r_ncsr_local_group_10.135
r_symmetry_xyhbond_nbd_refined0.113
r_chiral_restr0.098
r_symmetry_nbtor_other0.083
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5481
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms99

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing