9EQI | pdb_00009eqi

Hydrogenase-1 Ni-B state poised at +100mV

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4UE3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	296	100 mM tris pH 8.0, 200 mM LiSO4, 150 mM NaCl, 19-20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.548	α = 90
b = 97.209	β = 90
c = 182.823	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 EIGER X 16M		2022-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.7749	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.4	91.411	100	0.253	0.073	0.997	6.3	13.6		326125

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.42	100		2.9	0.83	0.529	0.7	14

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	1.4	91.411	325102	16257	99.723	0.157	0.1556	0.1573	0.1757	0.1812	16.032

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]
0.567			1.08		-1.647

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33
r_dihedral_angle_4_deg	18.023
r_dihedral_angle_3_deg	12.857
r_dihedral_angle_1_deg	6.495
r_lrange_it	4.624
r_lrange_other	4.624
r_scangle_it	3.386
r_scangle_other	3.385
r_scbond_it	2.253
r_scbond_other	2.252
r_angle_refined_deg	1.7
r_mcangle_it	1.621
r_mcangle_other	1.621
r_angle_other_deg	1.609
r_mcbond_it	1.165
r_mcbond_other	1.165
r_nbd_other	0.237
r_nbd_refined	0.223
r_symmetry_nbd_refined	0.189
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.165
r_symmetry_xyhbond_nbd_refined	0.16
r_symmetry_xyhbond_nbd_other	0.149
r_chiral_restr	0.091
r_metal_ion_refined	0.089
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13154
Nucleic Acid Atoms
Solvent Atoms	1726
Heterogen Atoms	76

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
REFMAC	phasing