5FEP

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293PEG 4000, Lithium sulfate, CHAPS, TrisHCl
Crystal Properties
Matthews coefficientSolvent content
2.1542.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.16α = 90
b = 80.02β = 90
c = 86.36γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.979ESRFBM30A

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
11.4544.0599.514.863.463460
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)
11.451.540.81

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 REPLACEMENTTHROUGHOUT3IIX1.4544.0260277318399.720.162890.161620.18797RANDOM21.714
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]
0.440.89-1.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.858
r_dihedral_angle_4_deg19.067
r_dihedral_angle_3_deg13.423
r_long_range_B_refined5.971
r_long_range_B_other5.971
r_dihedral_angle_1_deg5.593
r_scangle_other3.911
r_scbond_it2.713
r_scbond_other2.712
r_angle_refined_deg2.396
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.858
r_dihedral_angle_4_deg19.067
r_dihedral_angle_3_deg13.423
r_long_range_B_refined5.971
r_long_range_B_other5.971
r_dihedral_angle_1_deg5.593
r_scangle_other3.911
r_scbond_it2.713
r_scbond_other2.712
r_angle_refined_deg2.396
r_mcangle_it2.326
r_mcangle_other2.326
r_mcbond_it1.772
r_mcbond_other1.771
r_angle_other_deg1.251
r_chiral_restr0.154
r_bond_refined_d0.023
r_gen_planes_refined0.01
r_bond_other_d0.005
r_gen_planes_other0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2750
Nucleic Acid Atoms
Solvent Atoms485
Heterogen Atoms215

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing