8POV

Crystal Structure of the C19G/C120G variant of the membrane-bound [NiFe]-Hydrogenase from Cupriavidus necator in the H2-reduced state at 1.92 A Resolution.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RGW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	277	20% - 30% PEG3350, 0.1M BIS-TRIS PH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.02	38.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.201	α = 90
b = 95.506	β = 90
c = 118.978	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	CCD	RAYONIX MX-225		2012-01-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

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	1.92	34.2	100	0.091	9.9	4.9		64415

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.92	2.02	100		0.531	0.86	2.1	5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.92	34.2	60918	3245	99.69	0.16826	0.16656	0.19938	RANDOM	29.668

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]
-0.24			-1.5		1.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.4
r_sphericity_free	33.096
r_dihedral_angle_4_deg	16.956
r_dihedral_angle_3_deg	12.598
r_sphericity_bonded	6.676
r_dihedral_angle_1_deg	5.52
r_long_range_B_refined	3.458
r_long_range_B_other	3.458
r_mcangle_it	2.063
r_mcangle_other	2.063
r_scangle_other	1.766
r_rigid_bond_restr	1.616
r_mcbond_it	1.581
r_mcbond_other	1.581
r_scbond_it	1.47
r_scbond_other	1.47
r_angle_refined_deg	1.076
r_angle_other_deg	0.768
r_chiral_restr	0.061
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6780
Nucleic Acid Atoms
Solvent Atoms	530
Heterogen Atoms	32

Software

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