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SH3 domain of JNK-interacting Protein 1 (JIP1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FPE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293.15 0.1 M HEPES pH 7.5; 1-5 PEG 400; 2-2.5 M Ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.399 α = 90 b = 82.128 β = 90 c = 46.849 γ = 90
Symmetry Space Group P 21 21 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 2020-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.96546 ESRF ID30B
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 1.35 53.883 91.8 0.993 9.5 4.6 41308 1.5
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 1.356 1.48 0.61 1.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2FPE 1.45 53.883 40262 2066 81.147 0.16 0.1565 0.1546 0.215 0.2153 25.32
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] -0.969 1.907 -0.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.681 r_dihedral_angle_4_deg 19.746 r_dihedral_angle_3_deg 15.704 r_dihedral_angle_1_deg 8.553 r_lrange_it 6.956 r_scangle_it 6.844 r_scangle_other 6.842 r_lrange_other 6.828 r_scbond_it 5.808 r_scbond_other 5.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.681 r_dihedral_angle_4_deg 19.746 r_dihedral_angle_3_deg 15.704 r_dihedral_angle_1_deg 8.553 r_lrange_it 6.956 r_scangle_it 6.844 r_scangle_other 6.842 r_lrange_other 6.828 r_scbond_it 5.808 r_scbond_other 5.807 r_mcangle_other 5.044 r_mcangle_it 4.988 r_mcbond_it 4.372 r_mcbond_other 4.337 r_rigid_bond_restr 3.393 r_angle_refined_deg 1.689 r_angle_other_deg 1.418 r_symmetry_xyhbond_nbd_refined 0.288 r_symmetry_nbd_refined 0.252 r_nbd_other 0.235 r_nbd_refined 0.232 r_symmetry_nbd_other 0.203 r_xyhbond_nbd_refined 0.199 r_nbtor_refined 0.179 r_ncsr_local_group_4 0.126 r_ncsr_local_group_1 0.116 r_ncsr_local_group_6 0.11 r_ncsr_local_group_5 0.094 r_ncsr_local_group_3 0.088 r_chiral_restr 0.086 r_ncsr_local_group_2 0.083 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2069 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing