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Crystal structure of profilin from Dermatophagoides pteronyssinus in complex with a poly(L-proline) peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8TI5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1 M BIS-TRIS pH 6.5, 2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.89 57.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.802 α = 90 b = 152.802 β = 90 c = 186.854 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 EIGER X 16M 2022-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim 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 2.397 40 99.4 0.069 0.069 0.078 0.036 0.999 30.4 4.9 63158 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 99.7 0.662 0.662 0.735 0.318 0.687 2.1 5.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.397 34.161 63133 3203 98.846 0.167 0.1657 0.1657 0.1948 0.1922 74.893
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] -16.148 -16.148 32.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.947 r_dihedral_angle_3_deg 12.676 r_lrange_it 10.977 r_lrange_other 10.976 r_mcangle_it 8.715 r_mcangle_other 8.714 r_scangle_other 8.606 r_scangle_it 8.598 r_dihedral_angle_2_deg 6.959 r_dihedral_angle_1_deg 6.609
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.947 r_dihedral_angle_3_deg 12.676 r_lrange_it 10.977 r_lrange_other 10.976 r_mcangle_it 8.715 r_mcangle_other 8.714 r_scangle_other 8.606 r_scangle_it 8.598 r_dihedral_angle_2_deg 6.959 r_dihedral_angle_1_deg 6.609 r_mcbond_it 6.316 r_mcbond_other 6.314 r_scbond_it 6.221 r_scbond_other 6.179 r_chiral_restr_other 1.537 r_angle_refined_deg 1.373 r_angle_other_deg 1.057 r_symmetry_nbd_refined 0.242 r_symmetry_nbd_other 0.229 r_nbd_other 0.225 r_nbd_refined 0.207 r_nbtor_refined 0.177 r_ncsr_local_group_41 0.148 r_xyhbond_nbd_refined 0.147 r_ncsr_local_group_50 0.145 r_ncsr_local_group_46 0.14 r_ncsr_local_group_55 0.133 r_ncsr_local_group_35 0.132 r_ncsr_local_group_56 0.132 r_ncsr_local_group_53 0.13 r_ncsr_local_group_5 0.109 r_ncsr_local_group_15 0.109 r_ncsr_local_group_4 0.108 r_ncsr_local_group_7 0.106 r_ncsr_local_group_24 0.106 r_ncsr_local_group_19 0.104 r_ncsr_local_group_6 0.103 r_ncsr_local_group_2 0.102 r_ncsr_local_group_3 0.102 r_ncsr_local_group_22 0.102 r_ncsr_local_group_23 0.102 r_ncsr_local_group_26 0.102 r_ncsr_local_group_21 0.1 r_ncsr_local_group_37 0.1 r_ncsr_local_group_1 0.099 r_ncsr_local_group_18 0.099 r_ncsr_local_group_25 0.099 r_ncsr_local_group_17 0.097 r_ncsr_local_group_28 0.097 r_ncsr_local_group_8 0.096 r_ncsr_local_group_11 0.096 r_ncsr_local_group_14 0.096 r_ncsr_local_group_20 0.096 r_ncsr_local_group_13 0.095 r_ncsr_local_group_16 0.095 r_ncsr_local_group_27 0.095 r_ncsr_local_group_9 0.094 r_ncsr_local_group_10 0.093 r_ncsr_local_group_12 0.091 r_ncsr_local_group_42 0.089 r_symmetry_nbtor_other 0.084 r_ncsr_local_group_29 0.072 r_ncsr_local_group_36 0.072 r_ncsr_local_group_39 0.071 r_ncsr_local_group_38 0.07 r_ncsr_local_group_40 0.07 r_chiral_restr 0.068 r_ncsr_local_group_30 0.066 r_ncsr_local_group_44 0.066 r_ncsr_local_group_48 0.066 r_ncsr_local_group_43 0.063 r_ncsr_local_group_49 0.063 r_ncsr_local_group_47 0.062 r_ncsr_local_group_31 0.06 r_ncsr_local_group_45 0.058 r_symmetry_xyhbond_nbd_other 0.044 r_ncsr_local_group_33 0.036 r_ncsr_local_group_54 0.032 r_ncsr_local_group_51 0.024 r_ncsr_local_group_34 0.023 r_ncsr_local_group_52 0.023 r_ncsr_local_group_32 0.016 r_bond_refined_d 0.008 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8608 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing