7Y7N

Crystal structure of DUF371 domain-containing protein from Methanobrevibacter ruminantium

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291.15	12.00% w/v Polyethylene glycol 8,000,5.00% w/v Glycerol,100 mM Potassium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.354	α = 90
b = 47.354	β = 90
c = 135.877	γ = 90

Symmetry
Space Group	P 41 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		2022-01-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.97919	SSRF	BL18U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.76	44.72	100	0.09	0.1	0.043	0.999	12.3	9.3		16164

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.76	1.79			1.597	0.098	0.763	0.837		9.8

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3cbn	1.764	44.716	16016	781	99.919	0.226	0.224	0.2693	31.081

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]
1.011			1.011		-2.022

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.028
r_dihedral_angle_3_deg	14.188
r_dihedral_angle_4_deg	10.934
r_dihedral_angle_1_deg	7.39
r_lrange_other	7.194
r_lrange_it	7.192
r_scangle_it	6.078
r_scangle_other	6.074
r_scbond_it	4.03
r_scbond_other	4.03
r_mcangle_it	3.251
r_mcangle_other	3.249
r_mcbond_it	2.536
r_mcbond_other	2.531
r_angle_refined_deg	1.729
r_angle_other_deg	1.412
r_nbd_other	0.204
r_nbd_refined	0.2
r_symmetry_nbd_other	0.18
r_symmetry_nbd_refined	0.161
r_nbtor_refined	0.157
r_xyhbond_nbd_refined	0.149
r_symmetry_xyhbond_nbd_refined	0.111
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.079
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1076
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement