9ERS | pdb_00009ers

Hydrogenase-2 Ni-C state

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6EN9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	100 mM Tris 200 mM MgCl2 20% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.864	α = 90
b = 100.065	β = 90
c = 168.359	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		2023-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.8153	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	1.59	44.732	99.6	0.312	0.059	0.997	5.9	28.3		224817

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	1.59	1.62	98.4		3.84	0.75	0.502	0.3

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	1.59	44.732	224309	11098	99.315	0.174	0.1732	0.1864	0.1966	0.2083	22.168

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]
0.144			1.358		-1.503

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.293
r_dihedral_angle_3_deg	13.319
r_dihedral_angle_2_deg	6.584
r_dihedral_angle_1_deg	6.372
r_lrange_it	5.035
r_lrange_other	4.848
r_scangle_it	3.861
r_scangle_other	3.86
r_scbond_it	2.477
r_scbond_other	2.477
r_mcangle_it	2.17
r_mcangle_other	2.17
r_mcbond_it	1.558
r_mcbond_other	1.557
r_angle_refined_deg	1.353
r_angle_other_deg	0.47
r_chiral_restr_other	0.384
r_symmetry_xyhbond_nbd_other	0.252
r_nbd_other	0.234
r_symmetry_nbd_refined	0.233
r_nbd_refined	0.217
r_xyhbond_nbd_refined	0.206
r_symmetry_nbd_other	0.199
r_symmetry_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.177
r_metal_ion_refined	0.123
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.07
r_ncsr_local_group_1	0.06
r_ncsr_local_group_2	0.05
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12645
Nucleic Acid Atoms
Solvent Atoms	1353
Heterogen Atoms	101

Software

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