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structure of the core domaine of Knr4, an intrinsically disordered protein from Saccharomyces cerevisiae - mutant S200A S203A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5J1B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 285 PEG 3000 - 6000 15-24 % (w/v)
Bicine buffer 0.1 M
Crystal Properties Matthews coefficient Solvent content 2.29 46.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.816 α = 90 b = 102.816 β = 90 c = 92.7 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 PILATUS3 6M 2017-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97625 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim 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 2.35 45 99.8 0.052 0.056 0.999 19.2 7.1 23243
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.49 99.9 1.041 1.127 0.721 1.8 6.9
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 (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 5j1b 2.35 45 22073 1169 99.8 0.1963 0.1948 0.2417 0.22398 0.262 RANDOM 61.216
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] 2.86 1.43 2.86 -9.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.297 r_dihedral_angle_3_deg 14.654 r_dihedral_angle_4_deg 13.099 r_dihedral_angle_1_deg 6.425 r_long_range_B_refined 4.35 r_long_range_B_other 4.349 r_mcangle_it 2.61 r_mcangle_other 2.61 r_scangle_other 2.572 r_mcbond_it 1.553
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.297 r_dihedral_angle_3_deg 14.654 r_dihedral_angle_4_deg 13.099 r_dihedral_angle_1_deg 6.425 r_long_range_B_refined 4.35 r_long_range_B_other 4.349 r_mcangle_it 2.61 r_mcangle_other 2.61 r_scangle_other 2.572 r_mcbond_it 1.553 r_mcbond_other 1.551 r_scbond_it 1.535 r_scbond_other 1.535 r_angle_refined_deg 1.01 r_angle_other_deg 0.816 r_chiral_restr 0.049 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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 3513 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing