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Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methylene-tetrahydromethanopterin and coenzyme F420
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 2.48 50.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.148 α = 90 b = 165.539 β = 99.14 c = 93.552 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 2007-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9918 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 1.8 92.5 95.7 0.074 15.6 3.4 169214 -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 1.8 1.9 94.9 0.411 2.8 2.6 11198
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 1.8 92.45 -0.3 153747 8157 95.68 0.19162 0.18974 0.198 0.22771 0.2357 RANDOM 20.67
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 -1 0.78 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.789 r_dihedral_angle_4_deg 17.78 r_dihedral_angle_3_deg 16.185 r_dihedral_angle_1_deg 5.75 r_scangle_it 3.854 r_scbond_it 2.407 r_angle_other_deg 2.342 r_angle_refined_deg 1.627 r_mcangle_it 1.384 r_mcbond_it 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.789 r_dihedral_angle_4_deg 17.78 r_dihedral_angle_3_deg 16.185 r_dihedral_angle_1_deg 5.75 r_scangle_it 3.854 r_scbond_it 2.407 r_angle_other_deg 2.342 r_angle_refined_deg 1.627 r_mcangle_it 1.384 r_mcbond_it 0.82 r_mcbond_other 0.243 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13092 Nucleic Acid Atoms Solvent Atoms 634 Heterogen Atoms 457
Software Software Software Name Purpose AMoRE phasing REFMAC refinement XDS data reduction XDS data scaling