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X-ray Structure of the N-terminal Domain of Human Doublecortin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MG4 PDB ENTRY 1MG4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.4 1.4 M NAH2PO4, 0.35 M K2HPO4, 0.6% PEG 150, SITTING DROP, pH 4.40
Crystal Properties Matthews coefficient Solvent content 2.1 41.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.655 α = 90 b = 61.655 β = 90 c = 116.02 γ = 90
Symmetry Space Group I 4 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 CCD ADSC CCD 2003-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9B NSLS X9B
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 2.2 30 100 0.07 28.3 8.8 6002 36.9
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 2 2.28 100 0.48 4.6 8.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1MG4 2.2 40 5996 581 99.9 0.179 0.173 0.1745 0.237 0.2381 RANDOM 46.52
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] -0.247 -0.247 0.495
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.403 r_dihedral_angle_4_deg 16.199 r_dihedral_angle_3_deg 12.575 r_dihedral_angle_1_deg 5.438 r_scangle_it 2.968 r_angle_refined_deg 2.525 r_scbond_it 1.889 r_mcangle_it 1.118 r_mcbond_it 0.616 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.403 r_dihedral_angle_4_deg 16.199 r_dihedral_angle_3_deg 12.575 r_dihedral_angle_1_deg 5.438 r_scangle_it 2.968 r_angle_refined_deg 2.525 r_scbond_it 1.889 r_mcangle_it 1.118 r_mcbond_it 0.616 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.248 r_symmetry_vdw_refined 0.214 r_nbd_refined 0.187 r_xyhbond_nbd_refined 0.182 r_chiral_restr 0.121 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 781 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing