5NZX

Crystal structure of DNA cross-link repair protein 1A in complex with Ceftriaxone (alternative site)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP627830 % PEG 1000, 0.1 M MIB buffer pH 6.0
Crystal Properties
Matthews coefficientSolvent content
2.1242.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.45α = 90
b = 56.55β = 90
c = 113.52γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-01-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.4251.4397.50.0360.023117.65.861686
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)
11.421.4678.80.9850.7870.5121.13.4

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 REPLACEMENTTHROUGHOUT5aho1.4746.8653912284099.340.169640.16770.20666RANDOM27.61
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]
-0.281.09-0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.52
r_sphericity_free23.202
r_dihedral_angle_4_deg20.445
r_sphericity_bonded11.922
r_dihedral_angle_3_deg11.678
r_dihedral_angle_1_deg5.926
r_long_range_B_refined4.286
r_long_range_B_other4.285
r_scangle_other3.391
r_mcangle_other2.858
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.52
r_sphericity_free23.202
r_dihedral_angle_4_deg20.445
r_sphericity_bonded11.922
r_dihedral_angle_3_deg11.678
r_dihedral_angle_1_deg5.926
r_long_range_B_refined4.286
r_long_range_B_other4.285
r_scangle_other3.391
r_mcangle_other2.858
r_mcangle_it2.857
r_scbond_other2.725
r_scbond_it2.723
r_mcbond_it2.213
r_mcbond_other2.208
r_angle_refined_deg1.346
r_rigid_bond_restr1.221
r_angle_other_deg0.924
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.006
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2640
Nucleic Acid Atoms
Solvent Atoms206
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing