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Human Dihydropyrimidinase-related Protein 4 (DPYSL4, CRMP3, ULIP-4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BKN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.1 M Bis-tris-propane
0.2 M Sodium fluoride
10% Ethylene glycol
20% PEG3350
Crystal Properties Matthews coefficient Solvent content 1.95 36.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.47 α = 90 b = 102.65 β = 90 c = 116.99 γ = 90
Symmetry Space Group I 2 2 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 2014-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9797 Diamond I04
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 1.8 27.85 98.3 0.08 8.7 3 44328
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 1.8 1.84 96.6 0.651 2 2.9
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 THROUGHOUT 4BKN 1.8 77.16 42105 2200 98.03 0.1568 0.15452 0.1657 0.20049 0.2096 RANDOM 23.729
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] -1.69 2.04 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.116 r_dihedral_angle_4_deg 16.301 r_dihedral_angle_3_deg 13.163 r_dihedral_angle_1_deg 5.992 r_long_range_B_refined 5.875 r_long_range_B_other 5.762 r_scangle_other 4.33 r_scbond_it 2.922 r_scbond_other 2.921 r_mcangle_it 2.685
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.116 r_dihedral_angle_4_deg 16.301 r_dihedral_angle_3_deg 13.163 r_dihedral_angle_1_deg 5.992 r_long_range_B_refined 5.875 r_long_range_B_other 5.762 r_scangle_other 4.33 r_scbond_it 2.922 r_scbond_other 2.921 r_mcangle_it 2.685 r_mcangle_other 2.685 r_mcbond_it 1.904 r_mcbond_other 1.897 r_angle_refined_deg 1.831 r_angle_other_deg 1.055 r_chiral_restr 0.113 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 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 3698 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing