3IIX

X-ray structure of the FeFe-hydrogenase maturase HydE from T. maritima in complex with methionine and 5'deoxyadenosine


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
2.1843.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.054α = 90
b = 78.925β = 90
c = 86.192γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2008-05-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.976ESRFID29

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
11.2558.2295.10.04514.873.28853415
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)
1.251.3376.80.4072.11.4631571

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 3CIW1.2558.2288534467596.450.139960.138570.16623RANDOM11.993
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]
0.78-0.04-0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.744
r_dihedral_angle_1_deg18.802
r_dihedral_angle_4_deg15.557
r_dihedral_angle_3_deg12.431
r_sphericity_free5.033
r_scangle_it3.156
r_sphericity_bonded2.594
r_scbond_it2.366
r_mcangle_it1.73
r_angle_refined_deg1.675
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.744
r_dihedral_angle_1_deg18.802
r_dihedral_angle_4_deg15.557
r_dihedral_angle_3_deg12.431
r_sphericity_free5.033
r_scangle_it3.156
r_sphericity_bonded2.594
r_scbond_it2.366
r_mcangle_it1.73
r_angle_refined_deg1.675
r_rigid_bond_restr1.365
r_angle_other_deg1.256
r_mcbond_it1.234
r_mcbond_other0.498
r_nbd_refined0.254
r_symmetry_vdw_other0.243
r_nbd_other0.205
r_xyhbond_nbd_refined0.184
r_nbtor_refined0.179
r_symmetry_hbond_refined0.164
r_chiral_restr0.146
r_symmetry_vdw_refined0.087
r_nbtor_other0.085
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2877
Nucleic Acid Atoms
Solvent Atoms467
Heterogen Atoms200

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling