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Crystal structure of recombinant horse spleen apo-R168H/L169C-Fr
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DAT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 Ammonium Sulfate, Cadmium Sulfate
Crystal Properties Matthews coefficient Solvent content 3.2 61.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.644 α = 90 b = 182.644 β = 90 c = 182.644 γ = 90
Symmetry Space Group F 4 3 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 6M 2019-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.00 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.5 37.31 99.7 0.028 0.039 0.028 0.997 22.7 1.9 42065
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 0.039 0.055 0.039 0.995 1.9
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1dat 1.5 37.31 42065 2112 99.586 0.176 0.1751 0.1934 0.2273 14.462
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.575 r_dihedral_angle_4_deg 21.315 r_dihedral_angle_3_deg 12.851 r_lrange_it 5.242 r_dihedral_angle_1_deg 5.14 r_scangle_it 4.311 r_scbond_it 2.992 r_angle_refined_deg 2.217 r_mcangle_it 1.884 r_mcbond_it 1.286
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.575 r_dihedral_angle_4_deg 21.315 r_dihedral_angle_3_deg 12.851 r_lrange_it 5.242 r_dihedral_angle_1_deg 5.14 r_scangle_it 4.311 r_scbond_it 2.992 r_angle_refined_deg 2.217 r_mcangle_it 1.884 r_mcbond_it 1.286 r_nbtor_refined 0.312 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.201 r_symmetry_nbd_refined 0.191 r_symmetry_xyhbond_nbd_refined 0.141 r_chiral_restr 0.113 r_metal_ion_refined 0.03 r_symmetry_metal_ion_refined 0.03 r_bond_refined_d 0.015 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1363 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction Coot model building Aimless data scaling MOLREP phasing