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Crystal structure of Phm7 in complex with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7E5U Phm7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 1.54-1.62M Ammonium sulfate, 0.1M Tris HCl, 14-19% (v/v) Glycerol
Crystal Properties Matthews coefficient Solvent content 2.68 54.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.052 α = 90 b = 149.881 β = 97.119 c = 99.27 γ = 90
Symmetry Space Group C 1 2 1
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 2018-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.000000 SPring-8 BL32XU
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 1.61 45.216 99.82 0.996 12.59 3.5 169791
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 1.61 1.668 0.838
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 Phm7 1.61 45.216 169790 8514 99.827 0.184 0.1828 0.1921 0.2106 0.2164 25.514
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] 0.004 -0.002 0.001 -0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.296 r_dihedral_angle_4_deg 19.338 r_dihedral_angle_3_deg 12.564 r_dihedral_angle_1_deg 7.901 r_lrange_it 6.962 r_lrange_other 6.884 r_scangle_it 5.112 r_scangle_other 5.107 r_mcangle_it 3.827 r_mcangle_other 3.827
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.296 r_dihedral_angle_4_deg 19.338 r_dihedral_angle_3_deg 12.564 r_dihedral_angle_1_deg 7.901 r_lrange_it 6.962 r_lrange_other 6.884 r_scangle_it 5.112 r_scangle_other 5.107 r_mcangle_it 3.827 r_mcangle_other 3.827 r_scbond_it 3.447 r_scbond_other 3.445 r_mcbond_it 2.541 r_mcbond_other 2.541 r_angle_refined_deg 1.775 r_angle_other_deg 1.496 r_nbd_other 0.206 r_nbd_refined 0.199 r_symmetry_nbd_refined 0.193 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.152 r_symmetry_xyhbond_nbd_refined 0.128 r_symmetry_nbtor_other 0.094 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_symmetry_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8470 Nucleic Acid Atoms Solvent Atoms 792 Heterogen Atoms 192
Software Software Software Name Purpose XDS data reduction XDS data scaling pointless data scaling Aimless data scaling MLPHARE phasing Coot model building REFMAC refinement PHENIX refinement