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Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methenyl-tetrahydromethanopterin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QV9 PDB entry 1QV9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 30% PEG400, 0.1M MES, 0.1M sodium acetate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Crystal Properties Matthews coefficient Solvent content 2.57 52.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.4 α = 90 b = 167.1 β = 113.6 c = 122.5 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2009-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.008 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 112.5 99.2 0.062 14.9 4 256709 246709 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.1 77.6 0.511 2.7 77.6 35779
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1QV9 2.1 112.5 -3 208672 11021 99.23 0.16246 0.16048 0.1715 0.20028 0.2083 RANDOM 26.099
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 -0.06 0.77 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.654 r_dihedral_angle_4_deg 16.253 r_dihedral_angle_3_deg 15.432 r_dihedral_angle_1_deg 7.128 r_scangle_it 4.34 r_scbond_it 2.65 r_angle_refined_deg 1.631 r_mcangle_it 1.355 r_angle_other_deg 0.949 r_mcbond_it 0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.654 r_dihedral_angle_4_deg 16.253 r_dihedral_angle_3_deg 15.432 r_dihedral_angle_1_deg 7.128 r_scangle_it 4.34 r_scbond_it 2.65 r_angle_refined_deg 1.631 r_mcangle_it 1.355 r_angle_other_deg 0.949 r_mcbond_it 0.68 r_symmetry_metal_ion_refined 0.467 r_metal_ion_refined 0.447 r_symmetry_vdw_refined 0.406 r_symmetry_hbond_refined 0.308 r_mcbond_other 0.218 r_nbd_refined 0.216 r_symmetry_vdw_other 0.202 r_nbd_other 0.192 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.098 r_nbtor_other 0.089 r_xyhbond_nbd_other 0.079 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 26184 Nucleic Acid Atoms Solvent Atoms 1068 Heterogen Atoms 548
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XDS data scaling