3CUS

Structure of a double ILE/PHE mutant of NI-FE hydrogenase refined at 2.2 angstrom resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YQW	PDB ENTRY 1YQW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	PEG6000, GLYCEROL, PH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.4	α = 90
b = 99.96	β = 92.23
c = 182.69	γ = 90

Symmetry
Space Group	P 1 21 1

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	ADSC QUANTUM 315r	MIRRORS	2008-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.934	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.18	20	93.3	0.07	0.07	7.2	2.6	115860	108157			27

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.18	2.3	71		0.198	0.198	3.3	2.2	17163

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 1YQW	2.2	20	101754	5404	94.24	0.18677	0.18493	0.22223	RANDOM	15.032

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]
3.07		0.21	-0.93		-2.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.162
r_dihedral_angle_4_deg	14.543
r_dihedral_angle_3_deg	14.12
r_dihedral_angle_1_deg	9.521
r_angle_refined_deg	1.266
r_scangle_it	1.094
r_scbond_it	0.72
r_mcangle_it	0.602
r_mcbond_it	0.401
r_nbtor_refined	0.3
r_symmetry_vdw_refined	0.215
r_symmetry_hbond_refined	0.21
r_nbd_refined	0.196
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18418
Nucleic Acid Atoms
Solvent Atoms	1013
Heterogen Atoms	126

Software

Software
Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
ADSC	data collection
XDS	data reduction
XDS	data scaling