6EHQ | pdb_00006ehq

E. coli Hydrogenase-2 (as isolated form).

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5A4M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	100 mM Bis-tris pH 5.5 200 mM MgCl2 18-22% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.064	α = 90
b = 100.09	β = 90
c = 168.135	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 6M		2016-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.976	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.2	86	95.8	0.19	0.12	0.978	6.4	6.5		93703

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.24	95.5		0.98	0.63	0.68	1.7	6.2

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	5A4M	2.2	86	79987	4141	98.46	0.16365	0.16231	0.17	0.18951	0.2	RANDOM	29.825

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]
0.95			0.55		-1.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.165
r_dihedral_angle_4_deg	18.612
r_dihedral_angle_3_deg	12.507
r_dihedral_angle_1_deg	5.988
r_long_range_B_refined	3.775
r_long_range_B_other	3.747
r_scangle_other	2.76
r_mcangle_it	1.831
r_mcangle_other	1.831
r_scbond_it	1.667
r_scbond_other	1.667
r_angle_refined_deg	1.526
r_mcbond_it	1.137
r_mcbond_other	1.137
r_angle_other_deg	1.01
r_chiral_restr	0.092
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12647
Nucleic Acid Atoms
Solvent Atoms	525
Heterogen Atoms	64

Software

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