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X-ray structure of calcium-free human sorcin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JUO PDB ENTRY 1JUO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 20% PEG4000, 0.3 M AMMONIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 2.58 43.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.45 α = 90 b = 106.45 β = 90 c = 77.477 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 PIXEL DECTRIS PILATUS 2M M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R ELETTRA 5.2R
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 2.1 50 99.7 0.11 14.82 6.8 197835 1
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 2.1 2.2 98.2 0.59 3.61 7
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 1JUO 2.1 40.59 12641 673 99.96 0.18324 0.18144 0.1889 0.21974 0.2263 RANDOM 32.342
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] 0.32 0.32 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.283 r_dihedral_angle_4_deg 20.037 r_dihedral_angle_3_deg 17.708 r_dihedral_angle_1_deg 4.852 r_angle_refined_deg 1.462 r_angle_other_deg 0.846 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.283 r_dihedral_angle_4_deg 20.037 r_dihedral_angle_3_deg 17.708 r_dihedral_angle_1_deg 4.852 r_angle_refined_deg 1.462 r_angle_other_deg 0.846 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.004 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 1336 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing