☰ Navigation Tabs
Complex of human GDAP1 with hexadecanedioic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other GDAP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 M Lithium sulfate, 0.1 M bis-Tris pH 5.5, 25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.74 67.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.045 α = 90 b = 114.914 β = 90 c = 116.866 γ = 90
Symmetry Space Group P 21 21 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 XE 16M 2019-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9795 Diamond I24
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 2.2 45.63 99.7 0.998 12.72 6.6 50525
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 2.2 2.279 0.657
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE GDAP1 2.2 45.629 50524 2011 99.735 0.203 0.2022 0.2299 0.2376 70.524
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] -2.705 4.656 -1.952
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.468 r_dihedral_angle_4_deg 19.949 r_dihedral_angle_3_deg 16.677 r_lrange_it 11.846 r_lrange_other 11.846 r_scangle_it 6.935 r_scangle_other 6.877 r_dihedral_angle_1_deg 6.538 r_mcangle_other 5.202 r_mcangle_it 5.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.468 r_dihedral_angle_4_deg 19.949 r_dihedral_angle_3_deg 16.677 r_lrange_it 11.846 r_lrange_other 11.846 r_scangle_it 6.935 r_scangle_other 6.877 r_dihedral_angle_1_deg 6.538 r_mcangle_other 5.202 r_mcangle_it 5.2 r_scbond_it 4.678 r_scbond_other 4.568 r_mcbond_it 3.406 r_mcbond_other 3.4 r_angle_refined_deg 1.79 r_angle_other_deg 1.471 r_ext_dist_refined_d 0.354 r_symmetry_nbd_refined 0.273 r_nbd_other 0.251 r_nbd_refined 0.231 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.17 r_xyhbond_nbd_refined 0.161 r_ncsr_local_group_1 0.117 r_symmetry_xyhbond_nbd_other 0.094 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.081 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4162 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing