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Crystal structure of Mycobacterium avium dihydrofolate reductase in complex with NADPH and trimethoprim
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W3V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277.15 55% MPD, 0.1 M Hepes pH 7.5 and 2 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.46 49.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.251 α = 90 b = 70.251 β = 90 c = 73.511 γ = 90
Symmetry Space Group P 41 21 2
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 2019-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.97933 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2 29.564 99.4 0.024 0.034 0.024 0.999 14 1.8 12872
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 96.9 0.206 0.292 0.206 0.921 2.9 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2 29.564 12848 665 99.052 0.171 0.1666 0.1666 0.2403 0.2405 41.22
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] 1.722 1.722 -3.444
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.641 r_lrange_other 15.187 r_lrange_it 15.178 r_dihedral_angle_6_deg 13.582 r_dihedral_angle_3_deg 12.419 r_scangle_it 9.924 r_scangle_other 9.919 r_mcangle_it 8.409 r_mcangle_other 8.406 r_scbond_other 6.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.641 r_lrange_other 15.187 r_lrange_it 15.178 r_dihedral_angle_6_deg 13.582 r_dihedral_angle_3_deg 12.419 r_scangle_it 9.924 r_scangle_other 9.919 r_mcangle_it 8.409 r_mcangle_other 8.406 r_scbond_other 6.95 r_scbond_it 6.949 r_dihedral_angle_1_deg 6.699 r_mcbond_other 5.701 r_mcbond_it 5.697 r_rigid_bond_restr 4.45 r_angle_refined_deg 1.71 r_dihedral_angle_other_2_deg 0.64 r_angle_other_deg 0.555 r_symmetry_nbd_refined 0.406 r_nbd_other 0.311 r_nbd_refined 0.206 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.174 r_xyhbond_nbd_refined 0.144 r_symmetry_xyhbond_nbd_other 0.087 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1273 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement REFMAC refinement autoPROC data reduction XDS data reduction Aimless data scaling PHASER phasing