5A4I

The mechanism of Hydrogen activation by NiFE-hydrogenases

X-RAY DIFFRACTION

---

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 5.9, 22% (W/V) PEG 3350, 200 MM LISO4, 150 MM NACL, 1 MM TCEP, 0.02 % DDM

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.78	α = 90
b = 97.58	β = 90
c = 182.88	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	MIRRORS	2015-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

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	1.23	32.53	97.4	0.12	15.2	13.4		468877		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.23	1.26	94.9		1.3	13.3

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	1.23	32.19	445141	23652	97.2	0.12507	0.1239	0.14689	RANDOM	14.032

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]
0.16			0.28		-0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.225
r_sphericity_free	17.933
r_dihedral_angle_4_deg	16.799
r_dihedral_angle_3_deg	12.003
r_dihedral_angle_1_deg	6.123
r_sphericity_bonded	5.878
r_rigid_bond_restr	2.641
r_angle_refined_deg	1.895
r_scangle_it	1.834
r_scbond_it	1.794
r_mcangle_it	1.29
r_angle_other_deg	1.098
r_mcbond_it	1.086
r_mcbond_other	1.086
r_symmetry_vdw_refined	0.26
r_nbd_refined	0.243
r_nbd_other	0.225
r_symmetry_vdw_other	0.219
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.115
r_symmetry_hbond_refined	0.109
r_nbtor_other	0.096
r_metal_ion_refined	0.08
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
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	13170
Nucleic Acid Atoms
Solvent Atoms	935
Heterogen Atoms	104

Software

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