5A4F

The mechanism of Hydrogen Activation by NiFe-hydrogenases.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6		100 MM BIS-TRIS PH 6.0, 22% (W/V) PEG 3350, 200 MM LISO4, 150 MM NACL, 1 MM TCEP, 0.02 % (W/V) DDM

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.757	α = 90
b = 97.77	β = 90
c = 183.288	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 2M	MIRRORS	2015-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1		Diamond	I04-1

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	1.25	45.8	99.9	0.13	11.6	12		460946		-3

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	1.25	1.27	99.9		1.5	1.4	11.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3USC	1.25	91.64	437800	22969	99.84	0.12894	0.12752	0.15664	RANDOM	13.706

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]
0.23			0.25		-0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.952
r_sphericity_free	17.431
r_dihedral_angle_4_deg	16.713
r_dihedral_angle_3_deg	12.092
r_dihedral_angle_1_deg	6.133
r_sphericity_bonded	5.534
r_rigid_bond_restr	3.568
r_angle_refined_deg	1.938
r_scangle_it	1.833
r_scbond_it	1.779
r_mcangle_it	1.327
r_mcbond_it	1.13
r_mcbond_other	1.13
r_angle_other_deg	1.127
r_symmetry_vdw_refined	0.267
r_nbd_refined	0.244
r_nbd_other	0.225
r_symmetry_vdw_other	0.203
r_nbtor_refined	0.182
r_metal_ion_refined	0.139
r_xyhbond_nbd_refined	0.13
r_symmetry_hbond_refined	0.12
r_chiral_restr	0.117
r_nbtor_other	0.095
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13164
Nucleic Acid Atoms
Solvent Atoms	973
Heterogen Atoms	76

Software

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