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human SCBD (sorcin calcium binding domain) in complex with doxorubicin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UPG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 0.2 M MgCl2, 0.1 M Tris pH=7, NaCl 2.5 M
Crystal Properties Matthews coefficient Solvent content 3.63 66.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.229 α = 90 b = 104.831 β = 90 c = 113.273 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER R 4M 2016-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.74 76.94 99 0.102 0.998 11.81 6.53 11800
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 3.74 3.96 97.2 0.561 1.45 6.47
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 4UPG 3.74 76.94 11193 569 99.04 0.19623 0.19185 0.1989 0.28501 0.2923 RANDOM 177.223
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] -7.39 -1.22 8.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.362 r_long_range_B_refined 21.04 r_long_range_B_other 21.038 r_dihedral_angle_3_deg 20.699 r_dihedral_angle_4_deg 17.064 r_mcangle_it 15.746 r_mcangle_other 15.743 r_scangle_other 14.184 r_dihedral_angle_1_deg 10.988 r_mcbond_it 9.837
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.362 r_long_range_B_refined 21.04 r_long_range_B_other 21.038 r_dihedral_angle_3_deg 20.699 r_dihedral_angle_4_deg 17.064 r_mcangle_it 15.746 r_mcangle_other 15.743 r_scangle_other 14.184 r_dihedral_angle_1_deg 10.988 r_mcbond_it 9.837 r_mcbond_other 9.834 r_scbond_it 8.501 r_scbond_other 8.5 r_angle_refined_deg 1.324 r_angle_other_deg 1.001 r_chiral_restr 0.067 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 5226 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing