7C3S

Crystal structure of NE0047 (E143D) mutant in complex with 8-azaguanine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4HRQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.225M MgCl2, 25% PEG 3350, 0.1M Bis-Tris, PH 5.5
Crystal Properties
Matthews coefficientSolvent content
1.9135.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.491α = 90
b = 73.629β = 90
c = 109.997γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2016-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.98ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.665099.70.0550.0630.02922.84.437813
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.661.691000.4870.264

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4HRQ1.6636.3335915188999.970.161390.159750.19291RANDOM20.831
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.431
r_dihedral_angle_4_deg15.988
r_dihedral_angle_3_deg12.07
r_dihedral_angle_1_deg6.339
r_long_range_B_refined5.787
r_long_range_B_other5.778
r_scangle_other4.285
r_scbond_it2.957
r_scbond_other2.957
r_mcangle_it2.899
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.431
r_dihedral_angle_4_deg15.988
r_dihedral_angle_3_deg12.07
r_dihedral_angle_1_deg6.339
r_long_range_B_refined5.787
r_long_range_B_other5.778
r_scangle_other4.285
r_scbond_it2.957
r_scbond_other2.957
r_mcangle_it2.899
r_mcangle_other2.899
r_mcbond_it1.942
r_mcbond_other1.936
r_angle_refined_deg1.678
r_angle_other_deg1.55
r_chiral_restr0.079
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2666
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing