5FEZ

HydE from T. maritima in complex with (2R,4R)-MeSeTDA, 5'-deoxyadenosine and methionine

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	PEG4000, Lithium sulfate, CHAPS, TrisHCl

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.8	α = 90
b = 78.87	β = 90
c = 86.25	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		2014-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.979	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.35	44	99.8	15.27	5.9		76623

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	1.35	1.43			0.939

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	3IIX	1.35	38.27	72790	3833	99.87	0.11982	0.11904	0.12	0.13519	0.13	RANDOM	17.191

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]
1.29			-0.13		-1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.425
r_sphericity_free	32.399
r_dihedral_angle_4_deg	16.393
r_dihedral_angle_3_deg	11.887
r_sphericity_bonded	9.392
r_rigid_bond_restr	9.214
r_dihedral_angle_1_deg	5.946
r_long_range_B_refined	3.758
r_long_range_B_other	3.758
r_scangle_other	3.494
r_scbond_it	3.135
r_scbond_other	3.135
r_angle_refined_deg	2.277
r_mcangle_it	1.811
r_mcangle_other	1.811
r_mcbond_it	1.673
r_mcbond_other	1.673
r_angle_other_deg	1.434
r_chiral_restr	0.227
r_bond_refined_d	0.024
r_gen_planes_refined	0.012
r_gen_planes_other	0.005
r_bond_other_d	0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2741
Nucleic Acid Atoms
Solvent Atoms	502
Heterogen Atoms	215

Software

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