5NZW

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5AHO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		278	30% PEG 1000, 0.1 M MIB buffer pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.36

Crystal Data

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

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2016-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.972	ESRF	ID30B

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.7	40.5	99.6	0.1	0.046	0.999	10.1	6.2		9762

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)	Redundancy	Number Unique Reflections (All)
1	2.7	2.83	99.9		1.7	0.785	0.46	1.3	6.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5aho	2.7	40.5	9225	499	99.34	0.23056	0.22602	0.31504	RANDOM	88.151

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]
-5.49			7.34		-1.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.156
r_dihedral_angle_3_deg	16.461
r_dihedral_angle_4_deg	12.755
r_long_range_B_refined	12.47
r_long_range_B_other	12.468
r_mcangle_it	8.415
r_mcangle_other	8.415
r_scangle_other	8.276
r_dihedral_angle_1_deg	6.902
r_mcbond_it	5.458
r_mcbond_other	5.451
r_scbond_it	5.257
r_scbond_other	5.255
r_angle_refined_deg	1.453
r_angle_other_deg	0.939
r_chiral_restr	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	2625
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing