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structure of the core domaine of Knr4, an intrinsically disordered protein from Saccharomyces cerevisiae - mutant S200D
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, HANGING DROP 285 PEG 3000 - 6000 15-24 % (w/v)
Bicine buffer 0.1 M
Crystal Properties Matthews coefficient Solvent content 2.31 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.11 α = 90 b = 103.11 β = 90 c = 93.39 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 2015-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.976256 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 2.4 89.3 95.3 0.043 1 0.046 8 20213
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 2.4 2.46 68.9 1.226 1.345 0.46 1.3 5.8
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 2.4 45.18 20008 1080 95.3 0.18175 0.1798 0.2285 0.21691 0.2578 RANDOM 55.422
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] 0.01 0.01 0.01 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.999 r_dihedral_angle_3_deg 18.13 r_dihedral_angle_4_deg 13.745 r_dihedral_angle_1_deg 7.56 r_long_range_B_refined 5.431 r_long_range_B_other 5.431 r_scangle_other 4.272 r_mcangle_it 3.399 r_mcangle_other 3.399 r_scbond_it 2.761
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.999 r_dihedral_angle_3_deg 18.13 r_dihedral_angle_4_deg 13.745 r_dihedral_angle_1_deg 7.56 r_long_range_B_refined 5.431 r_long_range_B_other 5.431 r_scangle_other 4.272 r_mcangle_it 3.399 r_mcangle_other 3.399 r_scbond_it 2.761 r_scbond_other 2.758 r_mcbond_it 2.273 r_mcbond_other 2.273 r_angle_refined_deg 1.66 r_angle_other_deg 1.003 r_chiral_restr 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 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 3453 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data scaling PHASER phasing XDS data reduction