6YK9 | pdb_00006yk9

[Fe]-hydrogenase from Methanolacinia paynteri with bound guanylylpyridinol at 1.7-A resolution

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	8.5	283.15	[Fe]-hydrogenase holoenzyme from M. paynteri was crystallized under 95%N2/5%H2 at 283.15 K using 96-well two-drop MRC crystallization plates (sitting drop vapor diffusion method). 0.7 ul of 25-mg/ml reconstituted holoenzyme was mixed with 0.7-ul reservoir solution (from crystallization kits) under yellow light and incubated under dark conditions. The best diffracting crystal came out within two weeks in 25% w/v polyethylene glycol 1500 and 100 mM SPG buffer pH 8.5 (JBScreen Wizard 3&4 HTS, Jena Bioscience). For cryo protection, the crystal was soaked in the crystallization solution supplemented with 10% v/v glycerol.

Crystal Properties
Matthews coefficient	Solvent content
2	38.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 160.827	α = 90
b = 93.266	β = 97.53
c = 83.642	γ = 90

Symmetry
Space Group	C 1 2 1

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		2016-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.97970	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.7	82.92	99.1	0.107	0.125	0.065	0.993	8	3.7		133035			19.76

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.79	99.1		0.517	0.517	0.603	0.308	0.605	1.5	3.8

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	1.7	24.89	132993	6533	99	0.19	0.189	0.21	0.216	0.24	RANDOM	23.15

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]
-3.5604		-0.6402	1.2428		2.3176

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	13.51
t_omega_torsion	3.17
t_angle_deg	1.08
t_bond_d	0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
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	10393
Nucleic Acid Atoms
Solvent Atoms	1068
Heterogen Atoms	114

Software

Software
Software Name	Purpose
SCALA	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing