6IPF

Post-catalytic Complex of Human DNA Polymerase Mu with Templating Cytosine and Mn-8oxodGMP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.1 M HEPES pH 7.5, 18% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.778	α = 90
b = 68.792	β = 90
c = 109.62	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	CCD	RAYONIX MX-225		2018-05-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32XU	1	SPring-8	BL32XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.77	30	99.7	0.075	0.998	12.82	5.57		44400

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.77	1.88	98.9		0.77	0.794	2.13	5.68

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.77	30	42170	2267	99.74	0.18962	0.18811	0.21818	RANDOM	34.539

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]
-0.31			-1.38		1.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.79
r_dihedral_angle_4_deg	18.544
r_dihedral_angle_3_deg	11.899
r_long_range_B_refined	5.21
r_long_range_B_other	5.209
r_dihedral_angle_1_deg	4.991
r_scangle_other	3.106
r_mcangle_it	2.577
r_mcangle_other	2.576
r_scbond_it	2.008
r_scbond_other	2.007
r_mcbond_it	1.626
r_mcbond_other	1.626
r_angle_refined_deg	1.387
r_angle_other_deg	0.991
r_chiral_restr	0.07
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002
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 Atoms	Number
Protein Atoms	2560
Nucleic Acid Atoms	365
Solvent Atoms	278
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing