6SZD

Hydrogenase-2 variant R479K - hydrogen reduced form

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	6.5	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 = 99.424	α = 90
b = 100.564	β = 90
c = 168.658	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		2017-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92	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	1.5	100.5	97.8	0.086	0.11	0.07	0.997	8.4	4.3		262942

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	1.5	1.53	95.7		1.09	1.2	0.9	0.515	1.1	4.3

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	1.5	86.375	262802	13281	97.629	0.153	0.1518	0.1731	18.131

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]
0.816			0.122		-0.937

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.488
r_dihedral_angle_4_deg	19.299
r_dihedral_angle_3_deg	11.908
r_dihedral_angle_1_deg	6.475
r_lrange_it	4.606
r_lrange_other	4.524
r_scangle_it	3.851
r_scangle_other	3.845
r_scbond_it	2.581
r_scbond_other	2.55
r_mcangle_it	2.078
r_mcangle_other	2.077
r_angle_refined_deg	1.7
r_mcbond_it	1.552
r_mcbond_other	1.552
r_angle_other_deg	1.536
r_symmetry_xyhbond_nbd_other	0.332
r_nbd_refined	0.218
r_nbd_other	0.215
r_symmetry_nbd_other	0.174
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.155
r_symmetry_nbd_refined	0.13
r_chiral_restr	0.094
r_symmetry_nbtor_other	0.085
r_ncsr_local_group_2	0.058
r_ncsr_local_group_1	0.047
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
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	1226
Heterogen Atoms	75

Software

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