5NZW

Crystal structure of DNA cross-link repair protein 1A in complex with ceftriaxone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5AHO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP27830% PEG 1000, 0.1 M MIB buffer pH 6.0
Crystal Properties
Matthews coefficientSolvent content
2.1743.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.356α = 90
b = 58.495β = 90
c = 112.538γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.972ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
12.740.599.60.10.0460.99910.16.29762
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)
12.72.8399.91.70.7850.461.36.7

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 REPLACEMENTTHROUGHOUT5aho2.740.5922549999.340.230560.226020.31504RANDOM88.151
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]
-5.497.34-1.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.156
r_dihedral_angle_3_deg16.461
r_dihedral_angle_4_deg12.755
r_long_range_B_refined12.47
r_long_range_B_other12.468
r_mcangle_it8.415
r_mcangle_other8.415
r_scangle_other8.276
r_dihedral_angle_1_deg6.902
r_mcbond_it5.458
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.156
r_dihedral_angle_3_deg16.461
r_dihedral_angle_4_deg12.755
r_long_range_B_refined12.47
r_long_range_B_other12.468
r_mcangle_it8.415
r_mcangle_other8.415
r_scangle_other8.276
r_dihedral_angle_1_deg6.902
r_mcbond_it5.458
r_mcbond_other5.451
r_scbond_it5.257
r_scbond_other5.255
r_angle_refined_deg1.453
r_angle_other_deg0.939
r_chiral_restr0.075
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.002
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 Atoms2625
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing