9ER7 | pdb_00009er7

Hydrogenase-1 Ni-SCO state

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 pH8 200 mM LiSO4 150 mM NaCl 19-21% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.79	α = 90
b = 96.01	β = 90
c = 182.79	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		2022-05-05	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	66.2	99.4	0.27	0.055	0.999	6.3	14		322458

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	98.6		3.24	0.63	0.533	0.5	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	66.197	322458	16191	99.88	0.17	0.1686	0.1735	0.1894	0.195	18.372

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]
-0.521			2.109		-1.588

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.074
r_dihedral_angle_3_deg	11.935
r_dihedral_angle_2_deg	10.667
r_dihedral_angle_1_deg	6.486
r_lrange_it	4.803
r_lrange_other	4.667
r_scangle_it	3.665
r_scangle_other	3.651
r_scbond_it	2.428
r_scbond_other	2.418
r_mcangle_it	1.879
r_mcangle_other	1.879
r_angle_refined_deg	1.745
r_mcbond_it	1.413
r_mcbond_other	1.41
r_angle_other_deg	0.754
r_nbd_other	0.242
r_nbd_refined	0.229
r_symmetry_nbd_refined	0.212
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.141
r_symmetry_xyhbond_nbd_refined	0.129
r_metal_ion_refined	0.099
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.078
r_symmetry_xyhbond_nbd_other	0.031
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
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	1343
Heterogen Atoms	93

Software

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