☰ Navigation Tabs
Structure of Mth689, a DUF54 protein from Methanothermobacter thermautotrophicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OGK PDB ENTRY 2OGK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.2M LISO4, 0.1M HEPES PH 7.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.6 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.576 α = 90 b = 61.021 β = 90 c = 88.311 γ = 90
Symmetry Space Group P 21 21 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 315r 2006-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 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 1.95 25 99.9 0.07 18.3 6.2 24137 2.9 31
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 1.95 2.06 100 0.52 2.9 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2OGK 1.95 24.23 23631 515 99.98 0.19227 0.19104 0.228 0.24705 0.2778 RANDOM 37.8
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] -0.48 0.69 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.633 r_dihedral_angle_4_deg 19.226 r_dihedral_angle_3_deg 14.028 r_scangle_it 8.873 r_scbond_it 5.788 r_dihedral_angle_1_deg 5.678 r_mcangle_it 2.397 r_mcbond_it 1.485 r_angle_refined_deg 1.283 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.633 r_dihedral_angle_4_deg 19.226 r_dihedral_angle_3_deg 14.028 r_scangle_it 8.873 r_scbond_it 5.788 r_dihedral_angle_1_deg 5.678 r_mcangle_it 2.397 r_mcbond_it 1.485 r_angle_refined_deg 1.283 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2246 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing