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Crystal structure of two repeat fragment of reelin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DDU PDB ENTRY 2DDU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 7% PEG 3350, 75mM ammonium acetate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.52 51.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.008 α = 90 b = 70.953 β = 93.61 c = 94.769 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD ADSC QUANTUM 315 2005-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 94.491 96.4 0.075 0.075 9.6 4.1 77500 54041 25.2
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 2.07 98.73 0.075 3.5 4.1 51309
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-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 2DDU 2 47.29 51309 2732 98.73 0.21884 0.18125 0.17923 0.1805 0.21884 0.2223 RANDOM 28.264
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] 0.56 1.47 0.19 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.111 r_dihedral_angle_4_deg 14.135 r_dihedral_angle_3_deg 13.208 r_dihedral_angle_1_deg 6.628 r_scangle_it 2.311 r_scbond_it 1.442 r_angle_refined_deg 1.164 r_mcangle_it 0.984 r_mcbond_it 0.592 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.111 r_dihedral_angle_4_deg 14.135 r_dihedral_angle_3_deg 13.208 r_dihedral_angle_1_deg 6.628 r_scangle_it 2.311 r_scbond_it 1.442 r_angle_refined_deg 1.164 r_mcangle_it 0.984 r_mcbond_it 0.592 r_nbtor_refined 0.306 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.165 r_metal_ion_refined 0.128 r_xyhbond_nbd_refined 0.119 r_symmetry_hbond_refined 0.112 r_chiral_restr 0.076 r_bond_refined_d 0.009 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5550 Nucleic Acid Atoms Solvent Atoms 499 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing