8RSJ | pdb_00008rsj

Crystal structure of Methanobrevibacter oralis macrodomain in complex with ADPr in open conformation

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	200 mM sodium fluoride, 100 mM BisTris propane [pH 7.5], 20% (w/v) PEG3350< 1 M potassium sodium tartrate tetrahydrate

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.986	α = 90
b = 58.101	β = 117.664
c = 76.269	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS3 6M		2016-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.966000	ESRF	MASSIF-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	1.66	67.39	98.5	0.999	18.7	6		68604

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	1.66	1.69			0.873	3.3

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	1.66	67.39	68583	3322	98.34	0.194	0.1921	0.2009	0.2319	0.2366	24.098

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]
-1.216		0.871	-1.658		1.265

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.633
r_dihedral_angle_3_deg	14.805
r_dihedral_angle_2_deg	6.737
r_dihedral_angle_1_deg	6.541
r_lrange_it	5.7
r_lrange_other	5.533
r_scangle_it	3.059
r_scangle_other	3.059
r_chiral_restr_other	2.317
r_mcangle_other	2.3
r_mcangle_it	2.299
r_scbond_it	1.984
r_scbond_other	1.983
r_angle_refined_deg	1.662
r_mcbond_it	1.589
r_mcbond_other	1.582
r_angle_other_deg	0.737
r_symmetry_xyhbond_nbd_refined	0.225
r_nbd_refined	0.201
r_nbtor_refined	0.166
r_symmetry_nbd_other	0.158
r_xyhbond_nbd_refined	0.143
r_symmetry_nbd_refined	0.14
r_nbd_other	0.14
r_chiral_restr	0.122
r_metal_ion_refined	0.113
r_symmetry_nbtor_other	0.071
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4141
Nucleic Acid Atoms
Solvent Atoms	622
Heterogen Atoms	80

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing