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TLS refinement of the structure of Se-methionine labelled Coenzyme f420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) from Methanopyrus kandleri
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 MOPS, KOH, MPD, PEG 400, Mg acetate, Na phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.6 48.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.1 α = 90 b = 151.2 β = 90 c = 110 γ = 90
Symmetry Space Group C 2 2 21
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 2002-07-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9792, 0.9797, 0.95 ESRF ID14-4
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 1.54 20 99.1 0.075 17.7 3.5 145808 21.4
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) 1 1.54 1.62 99.9 0.257 3.9 3.5 15700
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.55 20 135825 135825 7207 99.1 0.17829 0.1778 0.19546 0.1951 RANDOM 13.914
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] 2.48 -1.72 -0.76
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.733 r_scbond_it 2.352 r_dihedral_angle_1_deg 2.098 r_angle_refined_deg 1.778 r_mcangle_it 1.148 r_mcbond_it 0.588 r_symmetry_vdw_refined 0.291 r_nbd_refined 0.236 r_symmetry_hbond_refined 0.172 r_xyhbond_nbd_refined 0.148
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.733 r_scbond_it 2.352 r_dihedral_angle_1_deg 2.098 r_angle_refined_deg 1.778 r_mcangle_it 1.148 r_mcbond_it 0.588 r_symmetry_vdw_refined 0.291 r_nbd_refined 0.236 r_symmetry_hbond_refined 0.172 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.133 r_metal_ion_refined 0.07 r_bond_refined_d 0.014 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6546 Nucleic Acid Atoms Solvent Atoms 580 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SHELXD phasing SHARP phasing