9FSA | pdb_00009fsa

Cell wall anchoring domain of the surface layer protein of Methanococcus voltae (aa 24-75; 484-576)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	293	JCSG+ eco condition C2 1.0 M LiCl, 0.1 M citrate pH 4.0, 20 % PEG 6000 0.3 ul condition + 0.3 ul protein solution

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.34	α = 90
b = 53.268	β = 90
c = 55.627	γ = 90

Symmetry
Space Group	P 2 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	PIXEL	Bruker PHOTON III		2024-06-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LIQUID ANODE	Excillum MetalJet D2+ 70 kV	1.3414

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.05	46.34	90.7	0.332	0.996	8.2	23.5		4977

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.24	70.1		1.8	0.65	1.6	15.8

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	2.05	46.34	4974	286	54.725	0.266	0.2652	0.27	0.2825	0.29	22.898

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]
-1.316			0.554		0.762

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.16
r_dihedral_angle_6_deg	16.086
r_lrange_it	8.812
r_lrange_other	8.812
r_dihedral_angle_1_deg	6.047
r_scangle_it	3.552
r_scangle_other	3.549
r_mcangle_it	3.505
r_mcangle_other	3.504
r_dihedral_angle_2_deg	3.029
r_mcbond_it	2.109
r_mcbond_other	2.107
r_scbond_it	2.054
r_scbond_other	2.052
r_angle_refined_deg	1.075
r_angle_other_deg	0.358
r_nbd_other	0.31
r_symmetry_nbd_refined	0.215
r_nbd_refined	0.205
r_symmetry_nbd_other	0.205
r_xyhbond_nbd_refined	0.205
r_nbtor_refined	0.168
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.044
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	928
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
DIALS	data reduction
STARANISO	data scaling
PHASER	phasing