8RSK | pdb_00008rsk

Crystal structure of Methanobrevibacter oralis macrodomain in complex with Asn-ADPr

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	5 mM zinc acetate, 9% (w/v) PEG8000, 100 mM sodium cocadylate pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.146	α = 90
b = 110.443	β = 119.559
c = 104.61	γ = 90

Symmetry
Space Group	C 1 2 1

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 PILATUS 6M		2017-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92819	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.359	69.955	99.9	0.993	7.3	3.1		42263

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.36	2.42			0.494	0.9

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.359	69.955	42051	1951	99.151	0.216	0.2134	0.2199	0.2607	0.2627	58.761

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]
0.475		0.736	-3.208		1.156

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.358
r_dihedral_angle_other_3_deg	16.985
r_dihedral_angle_6_deg	16.049
r_dihedral_angle_2_deg	10.207
r_lrange_other	8.491
r_lrange_it	8.483
r_dihedral_angle_1_deg	7.431
r_scangle_it	5.758
r_scangle_other	5.758
r_mcangle_it	4.577
r_mcangle_other	4.577
r_scbond_other	3.948
r_scbond_it	3.945
r_mcbond_it	2.927
r_mcbond_other	2.893
r_angle_refined_deg	2.211
r_angle_other_deg	0.683
r_nbd_other	0.45
r_symmetry_xyhbond_nbd_refined	0.291
r_nbd_refined	0.227
r_symmetry_nbd_refined	0.218
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.16
r_symmetry_metal_ion_refined	0.098
r_ncsr_local_group_3	0.095
r_chiral_restr	0.093
r_ncsr_local_group_2	0.093
r_ncsr_local_group_1	0.091
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.015
r_symmetry_xyhbond_nbd_other	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6225
Nucleic Acid Atoms
Solvent Atoms	174
Heterogen Atoms	185

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing