9GNK | pdb_00009gnk

Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from CpI of Clostridium pasteurianum

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	7.5	293	0.1 M HEPES pH 7.5, 20 % Polyethylene glycol 1500

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.137	α = 90
b = 89.213	β = 90
c = 106.449	γ = 90

Symmetry
Space Group	P 21 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	DECTRIS EIGER2 X 16M		2024-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	0.827	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	1.05	45.75	99.9	0.058	0.062	0.023	1	19.9	13.3		217266

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	1.05	1.07	99.6		1.737	1.881	0.716	0.581		13.2

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	1.05	45.75	217156	10877	99.838	0.169	0.1683	0.1686	0.1854	0.1856	13.675

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]
0.165			-0.163		-0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.597
r_dihedral_angle_3_deg	11.605
r_dihedral_angle_2_deg	8.175
r_dihedral_angle_1_deg	6.37
r_lrange_it	2.617
r_lrange_other	2.353
r_angle_refined_deg	1.604
r_mcangle_it	0.75
r_mcangle_other	0.75
r_scangle_it	0.698
r_scangle_other	0.698
r_angle_other_deg	0.498
r_mcbond_it	0.42
r_mcbond_other	0.42
r_scbond_it	0.407
r_scbond_other	0.407
r_nbd_refined	0.22
r_symmetry_nbd_other	0.198
r_nbd_other	0.184
r_nbtor_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.148
r_symmetry_nbd_refined	0.139
r_metal_ion_refined	0.099
r_chiral_restr	0.093
r_xyhbond_nbd_refined	0.086
r_symmetry_nbtor_other	0.076
r_bond_refined_d	0.004
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	3726
Nucleic Acid Atoms
Solvent Atoms	543
Heterogen Atoms	110

Software

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