3IQE

Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methylene-tetrahydromethanopterin and coenzyme F420


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QV9PDB ENTRY 1QV9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529130% PEG400, 0.1M MES, 0.1M sodium acetate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Crystal Properties
Matthews coefficientSolvent content
2.4850.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.148α = 90
b = 165.539β = 99.14
c = 93.552γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-09-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9918SLSX10SA

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
11.892.595.70.07415.63.4169214-3
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)
11.81.994.90.4112.82.611198

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 1QV91.892.45-0.3153747815795.680.191620.189740.22771RANDOM20.67
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]
-0.83-10.78-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.789
r_dihedral_angle_4_deg17.78
r_dihedral_angle_3_deg16.185
r_dihedral_angle_1_deg5.75
r_scangle_it3.854
r_scbond_it2.407
r_angle_other_deg2.342
r_angle_refined_deg1.627
r_mcangle_it1.384
r_mcbond_it0.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.789
r_dihedral_angle_4_deg17.78
r_dihedral_angle_3_deg16.185
r_dihedral_angle_1_deg5.75
r_scangle_it3.854
r_scbond_it2.407
r_angle_other_deg2.342
r_angle_refined_deg1.627
r_mcangle_it1.384
r_mcbond_it0.82
r_mcbond_other0.243
r_chiral_restr0.098
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13092
Nucleic Acid Atoms
Solvent Atoms634
Heterogen Atoms457

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling