☰ Navigation Tabs
Thermus thermophilus methylenetetrahydrofolate reductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3APT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.8 297 0.1M Hepes pH7.8, 1M LiCl, 20% PEG6k
Crystal Properties Matthews coefficient Solvent content 2.4 48.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.284 α = 90 b = 89.055 β = 90 c = 161.207 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 PIXEL DECTRIS EIGER X 9M 2021-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.1271 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.9 89.06 97.7 0.996 12.7 6.5 49988
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 0.965
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3apt 1.9 80.734 49922 2534 97.354 0.209 0.2065 0.207 0.2501 0.2509 30.143
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] 2.602 -0.995 -1.608
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.09 r_dihedral_angle_4_deg 20.208 r_dihedral_angle_3_deg 15.624 r_lrange_it 7.362 r_lrange_other 7.353 r_dihedral_angle_1_deg 6.31 r_scangle_it 5.374 r_scangle_other 5.373 r_mcangle_it 3.939 r_mcangle_other 3.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.09 r_dihedral_angle_4_deg 20.208 r_dihedral_angle_3_deg 15.624 r_lrange_it 7.362 r_lrange_other 7.353 r_dihedral_angle_1_deg 6.31 r_scangle_it 5.374 r_scangle_other 5.373 r_mcangle_it 3.939 r_mcangle_other 3.939 r_scbond_it 3.462 r_scbond_other 3.461 r_mcbond_other 2.669 r_mcbond_it 2.668 r_angle_refined_deg 1.594 r_angle_other_deg 1.318 r_symmetry_xyhbond_nbd_refined 0.339 r_symmetry_nbd_refined 0.285 r_nbd_refined 0.213 r_nbd_other 0.213 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.153 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.077 r_symmetry_xyhbond_nbd_other 0.063 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4489 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling REFMAC phasing