9ER5 | pdb_00009er5

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	293	100 mM tris pH 8 200 mM LiSO4 150 mM NaCl 19-21 % PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.62	α = 90
b = 97.36	β = 90
c = 182.96	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	86	100	0.27	0.07	0.998	6.6	13.9		328283

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	1.43	100		2.7	0.89	0.388	0.6	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	85.948	326983	16072	99.971	0.154	0.1534	0.1551	0.1735	0.1756	15.227

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]
0.095			1.144		-1.239

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.676
r_dihedral_angle_3_deg	14.325
r_dihedral_angle_2_deg	8.569
r_dihedral_angle_1_deg	6.475
r_lrange_it	4.376
r_lrange_other	4.256
r_scangle_it	3.643
r_scangle_other	3.643
r_scbond_other	2.453
r_scbond_it	2.452
r_angle_refined_deg	1.73
r_mcangle_it	1.728
r_mcangle_other	1.728
r_mcbond_it	1.299
r_mcbond_other	1.299
r_angle_other_deg	0.638
r_nbd_refined	0.225
r_symmetry_nbd_other	0.193
r_nbd_other	0.189
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.149
r_symmetry_nbd_refined	0.131
r_symmetry_xyhbond_nbd_refined	0.125
r_metal_ion_refined	0.107
r_chiral_restr	0.094
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13154
Nucleic Acid Atoms
Solvent Atoms	1338
Heterogen Atoms	71

Software

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