8RYH | pdb_00008ryh

Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits linked by a linker peptide derived from a group A1 type [FeFe]-hydrogenase of Veillonella atypica

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6SG2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.6	293	1 M Lithium chloride, 0.1 M Sodium acetate, 25 % Polyethylene glycol 4000

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.118	α = 90
b = 50.603	β = 105.331
c = 86.643	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 EIGER2 X 16M		2023-08-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.033	PETRA III, DESY	P11

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	1.77	45.402	96.4	0.159	0.187	0.098	0.996	8.9	6.9		41648

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	1.77	1.81	55.8		1.058	1.242	0.646	0.726	2.3	7

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	NONE	1.773	45.402	41647	2085	96.311	0.207	0.2048	0.2061	0.2461	0.2472	20.573

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]
0.903		-0.719	-1.054		0.473

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.291
r_dihedral_angle_3_deg	13.08
r_dihedral_angle_2_deg	9.625
r_dihedral_angle_1_deg	6.721
r_lrange_it	4.219
r_lrange_other	4.212
r_scangle_it	2.981
r_scangle_other	2.98
r_mcangle_other	2.365
r_mcangle_it	2.364
r_scbond_it	1.92
r_scbond_other	1.92
r_angle_refined_deg	1.861
r_mcbond_it	1.601
r_mcbond_other	1.6
r_angle_other_deg	0.569
r_nbd_refined	0.223
r_symmetry_nbd_other	0.211
r_nbd_other	0.195
r_nbtor_refined	0.181
r_symmetry_xyhbond_nbd_refined	0.179
r_symmetry_nbd_refined	0.137
r_xyhbond_nbd_refined	0.136
r_metal_ion_refined	0.116
r_chiral_restr	0.098
r_symmetry_nbtor_other	0.08
r_symmetry_xyhbond_nbd_other	0.03
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3602
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	41

Software

Software
Software Name	Purpose
REFMAC	refinement
BUCCANEER	model building
Coot	model building
PHASER	phasing
XDS	data reduction
Aimless	data scaling