5FES

HydE from T. maritima in complex with (2R,4R)-MeSeTDA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IIX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293PEG4000, Lithium sulfate, CHAPS, TrisHCl
Crystal Properties
Matthews coefficientSolvent content
2.1242.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.07α = 90
b = 79.1β = 90
c = 86.26γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.980ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.274499.110.772.992271
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.271.350.627

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3IIX1.2743.9587752451999.640.109030.107680.13526RANDOM17.792
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]
0.58-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.858
r_sphericity_free29.62
r_dihedral_angle_4_deg17.245
r_dihedral_angle_3_deg12.045
r_sphericity_bonded9.892
r_rigid_bond_restr7.3
r_dihedral_angle_1_deg6.235
r_long_range_B_refined3.708
r_long_range_B_other3.708
r_scangle_other3.183
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.858
r_sphericity_free29.62
r_dihedral_angle_4_deg17.245
r_dihedral_angle_3_deg12.045
r_sphericity_bonded9.892
r_rigid_bond_restr7.3
r_dihedral_angle_1_deg6.235
r_long_range_B_refined3.708
r_long_range_B_other3.708
r_scangle_other3.183
r_scbond_other2.979
r_scbond_it2.978
r_angle_refined_deg2.514
r_mcangle_it1.962
r_mcangle_other1.961
r_mcbond_it1.787
r_mcbond_other1.787
r_angle_other_deg1.313
r_chiral_restr0.18
r_bond_refined_d0.026
r_gen_planes_refined0.013
r_bond_other_d0.004
r_gen_planes_other0.003
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 AtomsNumber
Protein Atoms2735
Nucleic Acid Atoms
Solvent Atoms468
Heterogen Atoms215

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing