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co-crystal structure of non-carboxylic acid inhibitor with PHD2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QGV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M NH4 phosphate monobasic,0.1M Tris,8.5,50% MPD
Crystal Properties Matthews coefficient Solvent content 2.7 54.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.843 α = 90 b = 80.843 β = 90 c = 63.899 γ = 120
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 2021-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.18057 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 2.45 47.2 100 0.068 27.6 19.9 8837
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 2.45 2.55 1.05
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 2.451 47.2 8824 488 99.977 0.246 0.242 0.244 0.3084 0.3137 76.018
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] 0.638 0.319 0.638 -2.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.342 r_dihedral_angle_3_deg 10.998 r_dihedral_angle_1_deg 6.891 r_lrange_it 5.993 r_lrange_other 5.976 r_dihedral_angle_2_deg 4.155 r_mcangle_it 4.041 r_mcangle_other 4.039 r_scangle_it 3.724 r_scangle_other 3.723
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.342 r_dihedral_angle_3_deg 10.998 r_dihedral_angle_1_deg 6.891 r_lrange_it 5.993 r_lrange_other 5.976 r_dihedral_angle_2_deg 4.155 r_mcangle_it 4.041 r_mcangle_other 4.039 r_scangle_it 3.724 r_scangle_other 3.723 r_mcbond_other 2.663 r_mcbond_it 2.662 r_scbond_it 2.413 r_scbond_other 2.401 r_angle_refined_deg 0.756 r_angle_other_deg 0.268 r_nbd_refined 0.213 r_symmetry_nbd_refined 0.19 r_nbtor_refined 0.18 r_symmetry_nbd_other 0.179 r_nbd_other 0.168 r_xyhbond_nbd_refined 0.113 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.035 r_chiral_restr_other 0.02 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1569 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing