6SZK

Hydrogenase-2 variant R479K - hydrogen reduced form treated with CO

X-RAY DIFFRACTION

---

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.38

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	1.2	87.7	99.8	0.1	0.12	0.059	0.998	8.3	7.2		539529

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	1.2	1.22	97.3		1.4	1.6	0.83	0.657	1.2	7

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	1.2	86.7	538955	27288	99.904	0.122	0.1207	0.1414	15.141

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]
0.131			-0.296		0.165

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.315
r_dihedral_angle_4_deg	19.811
r_dihedral_angle_3_deg	11.447
r_dihedral_angle_1_deg	6.463
r_rigid_bond_restr	5.084
r_scangle_it	3.898
r_scangle_other	3.898
r_lrange_other	3.643
r_lrange_it	3.642
r_scbond_it	3.5
r_scbond_other	3.5
r_mcangle_it	2.265
r_mcangle_other	2.265
r_angle_refined_deg	2.126
r_mcbond_it	1.98
r_mcbond_other	1.979
r_angle_other_deg	1.63
r_nbd_refined	0.231
r_nbd_other	0.173
r_symmetry_nbd_other	0.17
r_nbtor_refined	0.16
r_symmetry_xyhbond_nbd_refined	0.141
r_xyhbond_nbd_refined	0.139
r_symmetry_xyhbond_nbd_other	0.137
r_chiral_restr	0.13
r_metal_ion_refined	0.126
r_symmetry_nbd_refined	0.111
r_symmetry_nbtor_other	0.089
r_bond_refined_d	0.019
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12650
Nucleic Acid Atoms
Solvent Atoms	1453
Heterogen Atoms	85

Software

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