6SYX

Hydrogenase-2 variant R479K - reduced sample exposed to pure oxygen

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	296	100mM Bis-tris pH 6.5, 200 mM MgCl2, 18-21% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.729	α = 90
b = 101.332	β = 90
c = 170.681	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 PILATUS 2M		2017-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9282	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.3	87.133	99.5	0.19	0.21	0.09	0.99	8	10.4		423495

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.32			1.94	2	0.93	0.776	1.5

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	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6en9	1.3	87.133	423263	20792	99.477	0.147	0.1466	0.1627	13.004

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]
0.268			0.217		-0.485

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.274
r_dihedral_angle_4_deg	20.101
r_dihedral_angle_3_deg	11.802
r_dihedral_angle_1_deg	6.477
r_lrange_it	4.985
r_lrange_other	4.632
r_scangle_it	3.686
r_scangle_other	3.686
r_scbond_it	2.436
r_scbond_other	2.436
r_angle_refined_deg	1.924
r_mcangle_it	1.724
r_mcangle_other	1.724
r_angle_other_deg	1.5
r_mcbond_it	1.209
r_mcbond_other	1.209
r_symmetry_xyhbond_nbd_refined	0.252
r_nbd_refined	0.22
r_symmetry_nbd_other	0.174
r_nbd_other	0.165
r_xyhbond_nbd_refined	0.162
r_metal_ion_refined	0.162
r_nbtor_refined	0.159
r_symmetry_xyhbond_nbd_other	0.123
r_chiral_restr	0.103
r_symmetry_nbd_refined	0.102
r_symmetry_nbtor_other	0.089
r_symmetry_metal_ion_refined	0.023
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12650
Nucleic Acid Atoms
Solvent Atoms	1809
Heterogen Atoms	114

Software

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