☰ Navigation Tabs
Crystal structure of DoxA in complex with reaction intermediate DHD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9S7F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 0.1M MES pH6.0; 0.2M NH4Cl; 20% (w/v) PEG6000
Crystal Properties Matthews coefficient Solvent content 2.49 50.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.873 α = 90 b = 108.058 β = 90 c = 179.772 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 PIXEL DECTRIS EIGER2 S 9M 2024-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 1 ESRF ID30B
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 2.54 89.89 99.4 0.304 0.359 0.188 0.874 2.9 6.6 32896
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 2.54 2.65 2.09 2.563 1.45 0.472 5.3
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 2.54 89.89 32714 1640 98.858 0.236 0.2335 0.2318 0.281 0.2761 69.427
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] -0.361 2.496 -2.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.739 r_dihedral_angle_6_deg 15.65 r_dihedral_angle_2_deg 15.312 r_lrange_it 9.104 r_lrange_other 9.088 r_dihedral_angle_1_deg 7.311 r_scangle_it 5.224 r_scangle_other 5.224 r_mcangle_it 4.882 r_mcangle_other 4.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.739 r_dihedral_angle_6_deg 15.65 r_dihedral_angle_2_deg 15.312 r_lrange_it 9.104 r_lrange_other 9.088 r_dihedral_angle_1_deg 7.311 r_scangle_it 5.224 r_scangle_other 5.224 r_mcangle_it 4.882 r_mcangle_other 4.881 r_scbond_it 3.183 r_scbond_other 3.182 r_mcbond_it 2.935 r_mcbond_other 2.935 r_angle_refined_deg 2.331 r_dihedral_angle_other_2_deg 2.11 r_angle_other_deg 0.778 r_symmetry_nbd_refined 0.36 r_nbd_other 0.317 r_symmetry_xyhbond_nbd_other 0.269 r_symmetry_xyhbond_nbd_refined 0.269 r_nbd_refined 0.262 r_xyhbond_nbd_refined 0.245 r_symmetry_nbd_other 0.227 r_nbtor_refined 0.199 r_symmetry_nbtor_other 0.094 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6287 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 162
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing