3IIZ | pdb_00003iiz

X-ray structure of the FeFe-hydrogenase maturase HydE from T. maritima in complex with S-adenosyl-L-methionine

X-RAY DIFFRACTION

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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
2.15	42.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.628	α = 90
b = 78.78	β = 90
c = 85.943	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 4		2005-06-20	M	SINGLE WAVELENGTH

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

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	1.62	43	93.5	0.066	13.39	2.5		41143			14

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)
	1.62	1.72	72.9		0.369	2.38	1.45	13887

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3CIW	1.62	38.16	41143	2204	97.58	0.1399	0.13754	0.15	0.18438	0.19	RANDOM	12.188

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]
0.62			0.06		-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.806
r_dihedral_angle_4_deg	15.901
r_dihedral_angle_3_deg	12.335
r_dihedral_angle_1_deg	11.92
r_sphericity_free	5.306
r_scangle_it	3.374
r_scbond_it	2.496
r_sphericity_bonded	2.43
r_angle_refined_deg	1.749
r_mcangle_it	1.616
r_rigid_bond_restr	1.598
r_mcbond_it	1.175
r_angle_other_deg	0.954
r_mcbond_other	0.424
r_nbd_refined	0.251
r_symmetry_vdw_other	0.243
r_nbd_other	0.211
r_symmetry_hbond_refined	0.208
r_xyhbond_nbd_refined	0.205
r_nbtor_refined	0.179
r_chiral_restr	0.099
r_symmetry_vdw_refined	0.098
r_nbtor_other	0.085
r_xyhbond_nbd_other	0.016
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2822
Nucleic Acid Atoms
Solvent Atoms	446
Heterogen Atoms	198

Software

Software
Software Name	Purpose
ProDC	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing