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Crystal Structure of Human Dihydropyrimidinease-like 2 (DPYSL2A)/Collapsin Response Mediator Protein (CRMP2 13-516) Mutant Y479E/Y499E
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GSE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 (0.2M magnesium chloride, 25% PEG 3350 and 0.1M bis-tris buffer pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.94 58.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.9 α = 90 b = 185.82 β = 90 c = 196.31 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 PILATUS 6M-F 2015-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.920 Diamond I04-1
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 2.48 83.98 99.92 0.989 6.21 6.8 46370
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2GSE 2.48 83.98 44041 2328 99.94 0.20851 0.20601 0.2145 0.25408 0.2562 RANDOM 39.954
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] 0.04 -0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.58 r_dihedral_angle_4_deg 20.298 r_dihedral_angle_3_deg 17.308 r_long_range_B_refined 7.871 r_long_range_B_other 7.871 r_dihedral_angle_1_deg 6.482 r_scangle_other 4.234 r_mcangle_other 3.795 r_mcangle_it 3.792 r_scbond_it 2.591
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.58 r_dihedral_angle_4_deg 20.298 r_dihedral_angle_3_deg 17.308 r_long_range_B_refined 7.871 r_long_range_B_other 7.871 r_dihedral_angle_1_deg 6.482 r_scangle_other 4.234 r_mcangle_other 3.795 r_mcangle_it 3.792 r_scbond_it 2.591 r_scbond_other 2.589 r_mcbond_it 2.392 r_mcbond_other 2.369 r_angle_refined_deg 1.667 r_angle_other_deg 1.042 r_chiral_restr 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7206 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing