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Crystal structure of SRCR domain 11 of DMBT1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6S5A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293.15 0.2 M Ammonium iodide, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 1.96 37.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.802 α = 90 b = 31.705 β = 90 c = 35.219 γ = 90
Symmetry Space Group P 21 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 2M-F 2022-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.00 Photon Factory AR-NE3A
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 1.51 40.9 98.7 0.999 27.02 2.94 22788
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.51 4.49 0.993
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 6S5A 1.51 40.9 13685 742 95.3 0.13999 0.13814 0.158 0.17225 0.1752 RANDOM 12.012
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 27.272 r_long_range_B_other 26.697 r_dihedral_angle_3_deg 13.828 r_dihedral_angle_1_deg 7.175 r_dihedral_angle_2_deg 5.092 r_scangle_other 3.063 r_mcangle_it 2.337 r_mcangle_other 2.336 r_scbond_it 2.074 r_scbond_other 2.033
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 27.272 r_long_range_B_other 26.697 r_dihedral_angle_3_deg 13.828 r_dihedral_angle_1_deg 7.175 r_dihedral_angle_2_deg 5.092 r_scangle_other 3.063 r_mcangle_it 2.337 r_mcangle_other 2.336 r_scbond_it 2.074 r_scbond_other 2.033 r_angle_refined_deg 1.714 r_mcbond_it 1.472 r_mcbond_other 1.442 r_angle_other_deg 0.661 r_chiral_restr 0.108 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 813 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing