3IIZ

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CIWPDB ENTRY 3CIW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5294PEG 4000, LISO4, TRIS pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.1542.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.628α = 90
b = 78.78β = 90
c = 85.943γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.934ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (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
11.624393.50.06613.392.54114314
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)
1.621.7272.90.3692.381.4513887

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3CIW1.6238.1641143220497.580.13990.137540.18438RANDOM12.188
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]
0.620.06-0.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.806
r_dihedral_angle_4_deg15.901
r_dihedral_angle_3_deg12.335
r_dihedral_angle_1_deg11.92
r_sphericity_free5.306
r_scangle_it3.374
r_scbond_it2.496
r_sphericity_bonded2.43
r_angle_refined_deg1.749
r_mcangle_it1.616
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.806
r_dihedral_angle_4_deg15.901
r_dihedral_angle_3_deg12.335
r_dihedral_angle_1_deg11.92
r_sphericity_free5.306
r_scangle_it3.374
r_scbond_it2.496
r_sphericity_bonded2.43
r_angle_refined_deg1.749
r_mcangle_it1.616
r_rigid_bond_restr1.598
r_mcbond_it1.175
r_angle_other_deg0.954
r_mcbond_other0.424
r_nbd_refined0.251
r_symmetry_vdw_other0.243
r_nbd_other0.211
r_symmetry_hbond_refined0.208
r_xyhbond_nbd_refined0.205
r_nbtor_refined0.179
r_chiral_restr0.099
r_symmetry_vdw_refined0.098
r_nbtor_other0.085
r_xyhbond_nbd_other0.016
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2822
Nucleic Acid Atoms
Solvent Atoms446
Heterogen Atoms198

Software

Software
Software NamePurpose
ProDCdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing