4UE3 | pdb_00004ue3

The Mechanism of Hydrogen Activation by NiFe-hydrogenases and the Importance of the active site Arginine

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	100 mM Bis tris pH 5.5-5.9, 150 mM NaCl 200 mM Li2SO4 19-21% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.521	α = 90
b = 97.405	β = 90
c = 183.229	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	2014-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.979	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	1.4	48.75	97	0.13	13.1	13.1		317004		-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	1.4	1.42	75.3		1.35	1.7	10.1

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3usc	1.4	48.75	316924	15658	96.835	0.141	0.1397	0.14	0.1602	0.16	12.322

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]
0.141			-0.046		-0.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.294
r_dihedral_angle_4_deg	16.799
r_dihedral_angle_3_deg	12.032
r_dihedral_angle_1_deg	6.558
r_lrange_it	4.012
r_lrange_other	3.918
r_scangle_it	3.187
r_scangle_other	3.187
r_scbond_other	2.147
r_scbond_it	2.146
r_angle_refined_deg	2.091
r_angle_other_deg	1.633
r_mcangle_it	1.464
r_mcangle_other	1.464
r_mcbond_other	1.033
r_mcbond_it	1.032
r_nbd_refined	0.234
r_symmetry_nbd_refined	0.234
r_symmetry_xyhbond_nbd_refined	0.229
r_nbd_other	0.214
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.157
r_metal_ion_refined	0.112
r_chiral_restr	0.103
r_symmetry_nbtor_other	0.087
r_symmetry_xyhbond_nbd_other	0.075
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13166
Nucleic Acid Atoms
Solvent Atoms	1340
Heterogen Atoms	87

Software

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