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Crystal structure of SRCRD11 of human DMBT1 from needle-shape crystal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SA5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293.15 0.2 M Lithium citrate tribasic tetrahydrate, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 3.19 61.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.114 α = 90 b = 71.114 β = 90 c = 55.387 γ = 120
Symmetry Space Group P 32 2 1
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 2021-11-24 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 2.54 41.18 99.73 0.998 13.12 5.11 8237
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 2.54 7.51 0.634
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 6AS5 2.54 41.18 5307 257 99.73 0.17923 0.17593 0.1853 0.24292 0.2466 RANDOM 56.817
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] 0.03 0.02 0.03 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.735 r_long_range_B_other 15.027 r_long_range_B_refined 14.969 r_scangle_other 9.294 r_dihedral_angle_1_deg 9.131 r_mcangle_it 7.797 r_mcangle_other 7.794 r_dihedral_angle_2_deg 7.757 r_scbond_it 6.774 r_scbond_other 6.683
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.735 r_long_range_B_other 15.027 r_long_range_B_refined 14.969 r_scangle_other 9.294 r_dihedral_angle_1_deg 9.131 r_mcangle_it 7.797 r_mcangle_other 7.794 r_dihedral_angle_2_deg 7.757 r_scbond_it 6.774 r_scbond_other 6.683 r_mcbond_it 5.818 r_mcbond_other 5.814 r_angle_refined_deg 1.585 r_angle_other_deg 0.616 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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 807 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing