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Crystal structure of ganglioside induced differentiation associated protein 2 (GDAP2) macro domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IQY PDB ENTRY 4IQY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 20% PEG3350, 10% ETHYLENE GLYCOL, 0.2 M SODIUM/POTASSIUM TARTRATE, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.4 48.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.84 α = 90 b = 70.84 β = 90 c = 97.549 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 PILATUS 6M 2014-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.9 26.57 100 0.1 13.7 10.5 20255
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 1.9 1.94 100 1.35 2.1 10.8
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4IQY 1.9 57.32 19218 993 99.9 0.1978 0.19608 0.23089 0.2334 RANDOM 37.014
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] 1.12 1.12 -2.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.751 r_dihedral_angle_4_deg 25.753 r_dihedral_angle_3_deg 14.243 r_dihedral_angle_1_deg 6.192 r_mcangle_it 3.8 r_scbond_it 3.051 r_mcbond_it 2.569 r_mcbond_other 2.567 r_angle_refined_deg 1.465 r_angle_other_deg 0.815
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.751 r_dihedral_angle_4_deg 25.753 r_dihedral_angle_3_deg 14.243 r_dihedral_angle_1_deg 6.192 r_mcangle_it 3.8 r_scbond_it 3.051 r_mcbond_it 2.569 r_mcbond_other 2.567 r_angle_refined_deg 1.465 r_angle_other_deg 0.815 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1557 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing