3IQF

Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methenyl-tetrahydromethanopterin


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
2.5752.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.4α = 90
b = 167.1β = 113.6
c = 122.5γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.008SLSX10SA

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
12112.599.20.06214.94256709246709-3
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)
122.177.60.5112.777.635779

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 1QV92.1112.5-32086721102199.230.162460.160480.20028RANDOM26.099
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]
-0.96-0.060.770.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.654
r_dihedral_angle_4_deg16.253
r_dihedral_angle_3_deg15.432
r_dihedral_angle_1_deg7.128
r_scangle_it4.34
r_scbond_it2.65
r_angle_refined_deg1.631
r_mcangle_it1.355
r_angle_other_deg0.949
r_mcbond_it0.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.654
r_dihedral_angle_4_deg16.253
r_dihedral_angle_3_deg15.432
r_dihedral_angle_1_deg7.128
r_scangle_it4.34
r_scbond_it2.65
r_angle_refined_deg1.631
r_mcangle_it1.355
r_angle_other_deg0.949
r_mcbond_it0.68
r_symmetry_metal_ion_refined0.467
r_metal_ion_refined0.447
r_symmetry_vdw_refined0.406
r_symmetry_hbond_refined0.308
r_mcbond_other0.218
r_nbd_refined0.216
r_symmetry_vdw_other0.202
r_nbd_other0.192
r_nbtor_refined0.176
r_xyhbond_nbd_refined0.169
r_chiral_restr0.098
r_nbtor_other0.089
r_xyhbond_nbd_other0.079
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms26184
Nucleic Acid Atoms
Solvent Atoms1068
Heterogen Atoms548

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling