7C3U

Crystal structure of NE0047 (N66A) 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 DROP2930.225 M MgCl2, 25% PEG 3350 and 0.1M BIS-TRIS, pH 5.5
Crystal Properties
Matthews coefficientSolvent content
1.935.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.186α = 90
b = 73.073β = 90
c = 109.942γ = 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)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
11.8660.8699.80.0680.0750.030.93225.8626490
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.861.8999.80.4840.220.932

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 REPLACEMENTTHROUGHOUT4HRQ1.8660.8624122126095.720.167480.16490.2169RANDOM20.684
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]
-0.020.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.522
r_dihedral_angle_4_deg19.304
r_dihedral_angle_3_deg13.314
r_dihedral_angle_1_deg5.932
r_long_range_B_refined5.306
r_long_range_B_other5.278
r_scangle_other4.012
r_scbond_it2.702
r_scbond_other2.701
r_mcangle_it2.541
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.522
r_dihedral_angle_4_deg19.304
r_dihedral_angle_3_deg13.314
r_dihedral_angle_1_deg5.932
r_long_range_B_refined5.306
r_long_range_B_other5.278
r_scangle_other4.012
r_scbond_it2.702
r_scbond_other2.701
r_mcangle_it2.541
r_mcangle_other2.541
r_angle_refined_deg1.864
r_mcbond_it1.766
r_mcbond_other1.759
r_angle_other_deg1.054
r_chiral_restr0.103
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms2644
Nucleic Acid Atoms
Solvent Atoms91
Heterogen Atoms28

Software

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