3IIX

X-ray structure of the FeFe-hydrogenase maturase HydE from T. maritima in complex with methionine and 5'deoxyadenosine

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	294	PEG 4000, LiSO4, TRIS pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.054	α = 90
b = 78.925	β = 90
c = 86.192	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	ADSC QUANTUM 315r		2008-05-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.976	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.25	58.22	95.1	0.045	14.87	3.2		88534			15

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.25	1.33	76.8		0.407	2.1	1.46	31571

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 3CIW	1.25	58.22	88534	4675	96.45	0.13996	0.13857	0.16623	RANDOM	11.993

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]
0.78			-0.04		-0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.744
r_dihedral_angle_1_deg	18.802
r_dihedral_angle_4_deg	15.557
r_dihedral_angle_3_deg	12.431
r_sphericity_free	5.033
r_scangle_it	3.156
r_sphericity_bonded	2.594
r_scbond_it	2.366
r_mcangle_it	1.73
r_angle_refined_deg	1.675
r_rigid_bond_restr	1.365
r_angle_other_deg	1.256
r_mcbond_it	1.234
r_mcbond_other	0.498
r_nbd_refined	0.254
r_symmetry_vdw_other	0.243
r_nbd_other	0.205
r_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.179
r_symmetry_hbond_refined	0.164
r_chiral_restr	0.146
r_symmetry_vdw_refined	0.087
r_nbtor_other	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2877
Nucleic Acid Atoms
Solvent Atoms	467
Heterogen Atoms	200

Software

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