8BJ7

Desulfovibrio desulfuricans FeFe Hydrogenase C178A mutant in Hinact-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	281.15	1 M Lithium chloride, 0.1 M Sodium acetate, 30 % Polyethylene glycol 4000

Crystal Properties
Matthews coefficient	Solvent content
1.8	31.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.328	α = 90
b = 87.281	β = 90
c = 88.977	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	1.04	44.528	99.7	0.119	0.999	10.9	13		183605

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	1.04	1.06			2.447	0.499	1.1

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	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6SG2	1.04	44.528	183502	9381	99.629	0.158	0.1577	0.1671	RANDOM	11.42

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]
0.624			-0.052		-0.572

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.378
r_dihedral_angle_3_deg	14.758
r_dihedral_angle_2_deg	7.502
r_dihedral_angle_1_deg	6.416
r_lrange_it	3.745
r_lrange_other	3.678
r_scangle_other	2.916
r_scangle_it	2.9
r_angle_refined_deg	2.144
r_scbond_other	2.022
r_scbond_it	2.007
r_mcangle_it	1.625
r_mcangle_other	1.625
r_mcbond_it	1.14
r_mcbond_other	1.137
r_angle_other_deg	1.047
r_symmetry_nbd_refined	0.278
r_nbd_refined	0.262
r_symmetry_xyhbond_nbd_refined	0.225
r_symmetry_nbd_other	0.206
r_nbtor_refined	0.188
r_nbd_other	0.18
r_chiral_restr	0.161
r_xyhbond_nbd_refined	0.108
r_metal_ion_refined	0.097
r_symmetry_nbtor_other	0.084
r_bond_other_d	0.044
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3721
Nucleic Acid Atoms
Solvent Atoms	440
Heterogen Atoms	43

Software

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