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The Crystal Structure of human SPR from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6I6C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.01M ZnCl2, 0.1M NaAc PH5, 20% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.27 41.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.893 α = 90 b = 74.56 β = 90 c = 121.176 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 PILATUS 6M 2020-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.00000 SPring-8 BL45XU
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 1.8 47.065 99.8 0.068 14.6 5.4 47688
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 1.8 1.84 0.435 2.3
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6I6C 1.8 47.065 47612 2289 99.759 0.195 0.1939 0.2029 0.2177 0.2255 24.486
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] -1.391 1.295 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.317 r_dihedral_angle_4_deg 19.329 r_dihedral_angle_3_deg 11.571 r_dihedral_angle_1_deg 5.965 r_lrange_it 3.53 r_lrange_other 3.442 r_scangle_it 1.604 r_scangle_other 1.604 r_mcangle_it 1.55 r_mcangle_other 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.317 r_dihedral_angle_4_deg 19.329 r_dihedral_angle_3_deg 11.571 r_dihedral_angle_1_deg 5.965 r_lrange_it 3.53 r_lrange_other 3.442 r_scangle_it 1.604 r_scangle_other 1.604 r_mcangle_it 1.55 r_mcangle_other 1.55 r_angle_refined_deg 1.318 r_angle_other_deg 1.156 r_scbond_it 0.963 r_scbond_other 0.963 r_mcbond_it 0.889 r_mcbond_other 0.887 r_symmetry_nbd_refined 0.265 r_symmetry_xyhbond_nbd_refined 0.223 r_nbd_refined 0.181 r_symmetry_nbd_other 0.164 r_nbd_other 0.155 r_nbtor_refined 0.136 r_xyhbond_nbd_refined 0.136 r_metal_ion_refined 0.085 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.047 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3895 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing