8RSI

Crystal structure of Methanobrevibacter oralis macrodomain

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	46.8 mM MES monohydrate, 53.2 mM imidazole, 20% (v/v) ethylene glycol, 10% (w/v) PEG8000

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.32	α = 90
b = 146.609	β = 90
c = 58.295	γ = 90

Symmetry
Space Group	P 21 21 2

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		2017-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	1.28229	Diamond	I03

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	2.059	146.39	100	0.992	6.7	12.1		38093

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	2.059	2.11			0.457	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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.059	73.412	37960	1799	99.478	0.195	0.1927	0.2437	45.758

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]
-1.076			1.585		-0.509

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.11
r_dihedral_angle_6_deg	15.447
r_lrange_it	8.276
r_lrange_other	8.275
r_dihedral_angle_2_deg	7.77
r_dihedral_angle_1_deg	6.413
r_scangle_it	6.243
r_scangle_other	6.243
r_mcangle_it	4.373
r_mcangle_other	4.372
r_scbond_it	4.227
r_scbond_other	4.167
r_mcbond_it	3.008
r_mcbond_other	3.007
r_angle_refined_deg	1.729
r_angle_other_deg	0.58
r_symmetry_nbd_refined	0.329
r_symmetry_xyhbond_nbd_refined	0.271
r_nbd_refined	0.23
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.181
r_nbd_other	0.179
r_metal_ion_refined	0.101
r_ncsr_local_group_1	0.091
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_chiral_restr_other	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4124
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	60

Software

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