6SG2 | pdb_00006sg2

FeFe Hydrogenase from Desulfovibrio desulfuricans in Hinact state

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HFE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.6	285	0.9 M LiCl, 26% PEG6000, 0.1 M sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
1.77	30.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.34	α = 90
b = 86.82	β = 90
c = 88.17	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 PILATUS3 6M		2018-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.65	43.45	100	0.158	10.6	13		46365			20.41

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.68	100		2.11		12.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1HFE	1.65	43.448	46300	2206	99.894	0.173	0.1709	0.18	0.2121	0.22	23.638

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]
1.606			-0.326		-1.279

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.942
r_dihedral_angle_4_deg	15.7
r_dihedral_angle_3_deg	13.238
r_dihedral_angle_1_deg	6.695
r_lrange_it	4.856
r_lrange_other	4.856
r_scangle_it	3.886
r_scangle_other	3.886
r_scbond_it	2.666
r_scbond_other	2.666
r_mcangle_it	2.467
r_mcangle_other	2.467
r_angle_refined_deg	2.307
r_angle_other_deg	2.129
r_mcbond_it	1.73
r_mcbond_other	1.728
r_nbd_other	0.256
r_nbd_refined	0.213
r_symmetry_xyhbond_nbd_other	0.205
r_symmetry_nbd_other	0.189
r_symmetry_nbd_refined	0.183
r_nbtor_refined	0.167
r_symmetry_xyhbond_nbd_refined	0.165
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3727
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing