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structure of the core domaine of Knr4, an intrinsically disordered protein from Saccharomyces cerevisiae - mutant S200D, S203D
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 2.25 45.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.38 α = 90 b = 102.38 β = 90 c = 92.336 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 2.15 45 99.5 0.062 0.068 0.997 13.3 5.2 29991
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 2.15 2.28 97 0.806 0.959 0.52 1.1 3.3
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 (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 2.15 44.81 28440 1550 99.47 0.19228 0.19085 0.2017 0.21852 0.2285 RANDOM 87.995
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] 0.72 0.36 0.72 -2.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.145 r_dihedral_angle_3_deg 15.278 r_dihedral_angle_4_deg 15.051 r_dihedral_angle_1_deg 7.098 r_long_range_B_other 5.595 r_long_range_B_refined 5.594 r_scangle_other 3.593 r_mcangle_it 3.303 r_mcangle_other 3.303 r_scbond_it 2.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.145 r_dihedral_angle_3_deg 15.278 r_dihedral_angle_4_deg 15.051 r_dihedral_angle_1_deg 7.098 r_long_range_B_other 5.595 r_long_range_B_refined 5.594 r_scangle_other 3.593 r_mcangle_it 3.303 r_mcangle_other 3.303 r_scbond_it 2.291 r_scbond_other 2.29 r_mcbond_other 2.096 r_mcbond_it 2.095 r_angle_refined_deg 1.256 r_angle_other_deg 0.928 r_chiral_restr 0.064 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 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 3526 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data scaling PHASER phasing XDS data reduction