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Mutant V517L of the SH3 domain of JNK-interacting protein 1 (JIP1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NYK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 0.1 M HEPES pH 7.5, 1-5 % PEG 400, 2-2.5 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.2 42.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.836 α = 90 b = 149.72 β = 105.834 c = 68.094 γ = 90
Symmetry Space Group C 1 2 1
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 Diamond beam splitter-monochromator 2020-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96545 ESRF MASSIF-1
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 1.959 67.659 97 0.988 8.5 2.7 47266
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 1.959 1.993 97.8 0.922 2.4
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 7NYK 1.959 67.659 47246 2330 86.843 0.227 0.2247 0.2415 0.281 0.2977 46.086
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] 0.12 -3.918 -0.479 2.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.399 r_dihedral_angle_3_deg 20.05 r_dihedral_angle_4_deg 17.452 r_lrange_it 9.776 r_lrange_other 9.776 r_dihedral_angle_1_deg 8.942 r_mcangle_it 4.003 r_mcangle_other 4.003 r_scangle_it 3.946 r_scangle_other 3.946
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.399 r_dihedral_angle_3_deg 20.05 r_dihedral_angle_4_deg 17.452 r_lrange_it 9.776 r_lrange_other 9.776 r_dihedral_angle_1_deg 8.942 r_mcangle_it 4.003 r_mcangle_other 4.003 r_scangle_it 3.946 r_scangle_other 3.946 r_scbond_it 2.426 r_scbond_other 2.423 r_mcbond_it 2.36 r_mcbond_other 2.36 r_angle_refined_deg 1.821 r_angle_other_deg 1.373 r_nbd_other 0.339 r_symmetry_nbd_refined 0.331 r_symmetry_xyhbond_nbd_refined 0.253 r_xyhbond_nbd_refined 0.236 r_symmetry_nbd_other 0.228 r_nbd_refined 0.214 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_other 0.142 r_ncsr_local_group_56 0.14 r_ncsr_local_group_66 0.136 r_ncsr_local_group_59 0.135 r_ncsr_local_group_11 0.133 r_ncsr_local_group_21 0.133 r_ncsr_local_group_38 0.133 r_ncsr_local_group_45 0.126 r_ncsr_local_group_30 0.125 r_ncsr_local_group_60 0.123 r_ncsr_local_group_63 0.122 r_ncsr_local_group_33 0.119 r_ncsr_local_group_37 0.118 r_ncsr_local_group_51 0.118 r_ncsr_local_group_52 0.118 r_ncsr_local_group_57 0.118 r_ncsr_local_group_31 0.116 r_ncsr_local_group_41 0.116 r_ncsr_local_group_50 0.116 r_ncsr_local_group_3 0.115 r_ncsr_local_group_17 0.113 r_ncsr_local_group_22 0.113 r_ncsr_local_group_64 0.113 r_ncsr_local_group_26 0.112 r_ncsr_local_group_7 0.111 r_ncsr_local_group_35 0.111 r_ncsr_local_group_16 0.11 r_ncsr_local_group_1 0.108 r_ncsr_local_group_13 0.108 r_ncsr_local_group_54 0.108 r_ncsr_local_group_36 0.107 r_ncsr_local_group_44 0.107 r_ncsr_local_group_46 0.107 r_ncsr_local_group_65 0.107 r_ncsr_local_group_9 0.106 r_ncsr_local_group_47 0.106 r_ncsr_local_group_14 0.105 r_ncsr_local_group_19 0.105 r_ncsr_local_group_43 0.105 r_ncsr_local_group_20 0.103 r_ncsr_local_group_12 0.102 r_ncsr_local_group_39 0.102 r_ncsr_local_group_10 0.101 r_ncsr_local_group_18 0.101 r_ncsr_local_group_32 0.101 r_ncsr_local_group_6 0.1 r_ncsr_local_group_5 0.099 r_ncsr_local_group_24 0.099 r_ncsr_local_group_58 0.098 r_ncsr_local_group_15 0.097 r_ncsr_local_group_29 0.096 r_ncsr_local_group_40 0.096 r_ncsr_local_group_48 0.095 r_ncsr_local_group_28 0.093 r_ncsr_local_group_61 0.093 r_ncsr_local_group_55 0.091 r_ncsr_local_group_34 0.087 r_ncsr_local_group_49 0.087 r_ncsr_local_group_42 0.086 r_ncsr_local_group_4 0.085 r_ncsr_local_group_25 0.085 r_ncsr_local_group_62 0.085 r_symmetry_nbtor_other 0.084 r_ncsr_local_group_8 0.083 r_ncsr_local_group_23 0.083 r_chiral_restr 0.082 r_ncsr_local_group_2 0.082 r_ncsr_local_group_27 0.081 r_ncsr_local_group_53 0.072 r_xyhbond_nbd_other 0.051 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.009 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6204 Nucleic Acid Atoms Solvent Atoms 574 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing