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The Crystal Structure of human DHFR from Biortus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BOZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.15M KBr, 30% PEGMME 2000
Crystal Properties Matthews coefficient Solvent content 1.9 35.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.569 α = 90 b = 61.569 β = 90 c = 94.068 γ = 90
Symmetry Space Group P 43 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 PILATUS3 6M 2021-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.521200 CLSI 08ID-1
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 1.85 47.03 100 0.114 15.9 11.2 16095
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 1.85 1.89 1.086
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 1BOZ 1.85 39.541 15956 791 99.352 0.243 0.2405 0.246 0.285 0.2914 32.357
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] 1.431 1.431 -2.861
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.833 r_dihedral_angle_3_deg 17.28 r_dihedral_angle_4_deg 13.944 r_dihedral_angle_1_deg 7.048 r_lrange_it 4.329 r_lrange_other 4.289 r_scangle_it 2.693 r_scangle_other 2.692 r_mcangle_it 2.585 r_mcangle_other 2.584
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.833 r_dihedral_angle_3_deg 17.28 r_dihedral_angle_4_deg 13.944 r_dihedral_angle_1_deg 7.048 r_lrange_it 4.329 r_lrange_other 4.289 r_scangle_it 2.693 r_scangle_other 2.692 r_mcangle_it 2.585 r_mcangle_other 2.584 r_scbond_it 1.61 r_scbond_other 1.609 r_mcbond_it 1.587 r_mcbond_other 1.586 r_angle_refined_deg 1.471 r_angle_other_deg 1.136 r_nbd_other 0.221 r_nbd_refined 0.195 r_symmetry_nbd_other 0.193 r_symmetry_nbd_refined 0.172 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.136 r_symmetry_nbtor_other 0.075 r_symmetry_xyhbond_nbd_other 0.07 r_chiral_restr 0.056 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1495 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing