6HAC | pdb_00006hac

Crystal structure of [Fe]-hydrogenase (Hmd) holoenzyme from Methanococcus aeolicus (open form)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JJF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	281.15	The reconstituted [Fe]-hydrogenase holoenzyme from M. aeolicus was crystallized in the anaerobic tent with gas phase 95%N2/5%H2 using 96-well 2-drop MRC Crystallization Plates (Molecular Dimensions, Suffolk, UK). For the initial screening, 0.7-ul of 24 mg/ml reconstituted [Fe]-hydrogenase was mixed with 0.7 ul of reservoir solution of crystallization kits under yellow light and incubated under the dark condition. The best diffracting crystal was obtained in one month in the crystallization reservoir solution containing 20% w/v polyethylene glycol 3350, 100-mM tri-sodium citrate pH 4.0 and 200-mM tri-sodium citrate.

Crystal Properties
Matthews coefficient	Solvent content
3.74	67.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.985	α = 90
b = 136.985	β = 90
c = 117.317	γ = 90

Symmetry
Space Group	I 41 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2016-09-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.97980	ESRF	BM30A

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	2.3	48.43	100	0.155	0.161	0.043	0.999	17.9	13.7		25078			39.33

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	2.3	2.42	100		1.023	1.061	0.281	0.602	2.9	14

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4JJF	2.3	26.62	25043	1229	100	0.172	0.171	0.18	0.192	0.2	RANDOM	43.63

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]
2.5933			2.5933		-5.1866

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	13.75
t_omega_torsion	2.27
t_angle_deg	1.11
t_bond_d	0.009
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2567
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	66

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing