6SYO

Hydrogenase-2 variant R479K - As Isolated form

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	296	100 mM Bis Tris pH 6.5, 200 mM MgCl2, 18-22% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.667	α = 90
b = 101.21	β = 90
c = 170.826	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	1.25	86.8	99.4	0.107	0.122	0.059	0.998	9	8.1		477343

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	1.25	1.27	91.5		1.64	1.92	0.97	0.553	1.1	7.2

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	1.25	85.559	477111	23819	99.87	0.115	0.1139	0.1361	14.967

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]
0.441			0.035		-0.476

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.29
r_dihedral_angle_4_deg	19.662
r_dihedral_angle_3_deg	11.687
r_dihedral_angle_1_deg	6.506
r_rigid_bond_restr	5.138
r_scangle_it	3.096
r_scangle_other	3.096
r_lrange_it	2.947
r_lrange_other	2.947
r_scbond_it	2.909
r_scbond_other	2.909
r_angle_refined_deg	2.136
r_mcangle_it	1.706
r_mcangle_other	1.706
r_angle_other_deg	1.562
r_mcbond_it	1.549
r_mcbond_other	1.549
r_symmetry_xyhbond_nbd_refined	0.265
r_nbd_refined	0.226
r_nbd_other	0.203
r_symmetry_nbd_other	0.173
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.154
r_symmetry_xyhbond_nbd_other	0.144
r_chiral_restr	0.122
r_metal_ion_refined	0.122
r_symmetry_nbtor_other	0.09
r_symmetry_nbd_refined	0.07
r_bond_refined_d	0.019
r_gen_planes_refined	0.013
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	1737
Heterogen Atoms	83

Software

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