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Crystal structure of the C-terminal domain of Schizosaccharomyces pombe FKBP nucleoplasmin SpAni2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Q10175
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 200 mM KCl,
50 mM HEPES (pH 7.5),
35% v/v Pentaerythritol propoxylate (5/4 PO/OH)
Crystal Properties Matthews coefficient Solvent content 3.5 64.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.097 α = 90 b = 113.097 β = 90 c = 221.042 γ = 120
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 X 4M 2023-05-11 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) 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 2.49 47.86 97.42 0.99 13.6 5.8 20100
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 2.49 2.59 0.87
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.488 47.859 18956 861 97.415 0.199 0.198 0.2029 0.2261 0.2374 RANDOM 49.283
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] -0.172 -0.086 -0.172 0.559
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.294 r_dihedral_angle_6_deg 16.516 r_lrange_it 8.618 r_lrange_other 8.617 r_dihedral_angle_1_deg 8.318 r_scangle_it 6.938 r_scangle_other 6.936 r_mcangle_it 5.043 r_mcangle_other 5.042 r_scbond_it 4.275
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.294 r_dihedral_angle_6_deg 16.516 r_lrange_it 8.618 r_lrange_other 8.617 r_dihedral_angle_1_deg 8.318 r_scangle_it 6.938 r_scangle_other 6.936 r_mcangle_it 5.043 r_mcangle_other 5.042 r_scbond_it 4.275 r_scbond_other 4.274 r_mcbond_it 3.212 r_mcbond_other 3.21 r_angle_refined_deg 1.871 r_angle_other_deg 0.595 r_nbd_refined 0.227 r_nbd_other 0.213 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.153 r_ncsr_local_group_2 0.152 r_ncsr_local_group_1 0.151 r_ncsr_local_group_3 0.133 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.089 r_bond_refined_d 0.023 r_symmetry_xyhbond_nbd_refined 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2689 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB-REDO refinement XDS data reduction Aimless data scaling MOLREP phasing