8BJ8

Desulfovibrio desulfuricans FeFe Hydrogenase C178A mutant in Htrans-like state

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	295.15	1 M Lithium chloride, 0.1 M Sodium acetate, 30 % Polyethylene glycol 4000

Crystal Properties
Matthews coefficient	Solvent content
1.81	31.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.387	α = 90
b = 87.411	β = 90
c = 89.125	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		2022-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	0.8266	PETRA III, DESY	P11

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	1.01	44.602	99.3	0.087	1	13.9	12.6		200463

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	1.01	1.03	93.4		2.148	0.338	0.9	8.7

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	6SG2	1.01	44.602	200362	9803	99.259	0.151	0.1502	0.1628	10.456

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]
0.257			-0.115		-0.142

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.386
r_dihedral_angle_3_deg	14.327
r_dihedral_angle_2_deg	8.03
r_dihedral_angle_1_deg	6.358
r_lrange_it	2.926
r_lrange_other	2.817
r_scangle_other	2.459
r_scangle_it	2.443
r_angle_refined_deg	2.089
r_scbond_other	1.732
r_scbond_it	1.716
r_mcangle_it	1.388
r_mcangle_other	1.388
r_mcbond_it	0.983
r_mcbond_other	0.98
r_angle_other_deg	0.693
r_nbd_refined	0.244
r_nbd_other	0.232
r_symmetry_nbd_other	0.2
r_symmetry_nbd_refined	0.197
r_nbtor_refined	0.187
r_chiral_restr	0.167
r_symmetry_xyhbond_nbd_refined	0.115
r_metal_ion_refined	0.099
r_xyhbond_nbd_refined	0.093
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3684
Nucleic Acid Atoms
Solvent Atoms	451
Heterogen Atoms	43

Software

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