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Crystal structure of methylenetetrahydromethanopterin reductase (Mer) in complex with coenzyme F420
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F07 PDB entry 1F07
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 281 Tris/HCl, PEG 4000, Isopropanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties Matthews coefficient Solvent content 2.38 46.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.81 α = 90 b = 83.41 β = 91.15 c = 99.17 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 ADSC QUANTUM 4 2004-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9792 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.6 30 97.1 0.085 14.2 3.96 40607 40607 37.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.6 2.74 86.4 0.214 6.8 3.6 5785
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1F07 2.61 19.95 40216 40216 2011 98.8 0.19 0.1851 0.185 0.1839 0.222 0.2218 RANDOM 28.7
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] -0.5 -1.57 3 -2.5
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.3 c_scangle_it 4.39 c_scbond_it 3.04 c_mcangle_it 2.63 c_mcbond_it 1.67 c_angle_deg 1.6 c_improper_angle_d 1.28 c_bond_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9684 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 231
Software Software Software Name Purpose DENZO data reduction XDS data reduction EPMR phasing CNS refinement XDS data scaling