3CIX

X-RAY structure of the [FeFe]-hydrogenase maturase HydE from thermotoga maritima in complex with thiocyanate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293PEG4000 35%, 100mM TrisHCl, pH8.5, 100mM LiSO4, 3mM CHAPS, 20mg/mL Protein, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1943.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.927α = 90
b = 79.728β = 90
c = 86.077γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42006-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.933ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.758.5295.80.07615.96.63749917.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7977.40.4133.45.24270

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 3CIW1.732.8735563189395.350.148340.14620.18865RANDOM13.913
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]
0.920.02-0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.602
r_dihedral_angle_4_deg13.636
r_dihedral_angle_1_deg12.242
r_dihedral_angle_3_deg11.999
r_sphericity_free5.854
r_scangle_it3.541
r_scbond_it2.5
r_sphericity_bonded2.482
r_rigid_bond_restr2.137
r_angle_refined_deg1.746
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.602
r_dihedral_angle_4_deg13.636
r_dihedral_angle_1_deg12.242
r_dihedral_angle_3_deg11.999
r_sphericity_free5.854
r_scangle_it3.541
r_scbond_it2.5
r_sphericity_bonded2.482
r_rigid_bond_restr2.137
r_angle_refined_deg1.746
r_mcangle_it1.65
r_mcbond_it1.2
r_angle_other_deg0.998
r_mcbond_other0.462
r_symmetry_vdw_refined0.313
r_symmetry_vdw_other0.25
r_nbd_refined0.216
r_nbd_other0.207
r_symmetry_hbond_refined0.2
r_xyhbond_nbd_refined0.184
r_nbtor_refined0.173
r_chiral_restr0.114
r_nbtor_other0.084
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2731
Nucleic Acid Atoms
Solvent Atoms366
Heterogen Atoms209

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling