☰ Navigation Tabs
Crystal structure of BbKI complexed with Human Kallikrein 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JOD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 25% PEG3350, 0.2M NaCl
Crystal Properties Matthews coefficient Solvent content 2.92 57.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.143 α = 90 b = 117.195 β = 89.571 c = 159.417 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 16M 2019-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.1 50 97.4 0.065 15.93 3.4 192940
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 1.057 1.9
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 7jod 2.1 49.494 170422 1650 86.387 0.184 0.1839 0.1913 0.2122 0.2165 33.785
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] 0.208 -0.087 -0.28 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.35 r_dihedral_angle_4_deg 19.935 r_lrange_other 15.996 r_dihedral_angle_3_deg 15.979 r_lrange_it 15.961 r_scangle_it 13.199 r_scangle_other 13.199 r_scbond_it 9.721 r_scbond_other 9.714 r_mcangle_other 8.938
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.35 r_dihedral_angle_4_deg 19.935 r_lrange_other 15.996 r_dihedral_angle_3_deg 15.979 r_lrange_it 15.961 r_scangle_it 13.199 r_scangle_other 13.199 r_scbond_it 9.721 r_scbond_other 9.714 r_mcangle_other 8.938 r_mcangle_it 8.937 r_dihedral_angle_1_deg 7.131 r_mcbond_it 6.771 r_mcbond_other 6.766 r_angle_refined_deg 1.518 r_symmetry_xyhbond_nbd_refined 0.444 r_angle_other_deg 0.418 r_symmetry_nbd_refined 0.395 r_nbd_other 0.331 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.191 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.166 r_symmetry_xyhbond_nbd_other 0.121 r_symmetry_nbtor_other 0.095 r_ncsr_local_group_18 0.091 r_ncsr_local_group_30 0.089 r_ncsr_local_group_8 0.087 r_ncsr_local_group_27 0.086 r_ncsr_local_group_28 0.086 r_ncsr_local_group_29 0.079 r_chiral_restr 0.066 r_ncsr_local_group_38 0.063 r_ncsr_local_group_17 0.062 r_ncsr_local_group_6 0.06 r_ncsr_local_group_21 0.058 r_ncsr_local_group_4 0.055 r_ncsr_local_group_12 0.055 r_ncsr_local_group_42 0.055 r_gen_planes_refined 0.054 r_ncsr_local_group_1 0.053 r_ncsr_local_group_11 0.053 r_ncsr_local_group_41 0.053 r_ncsr_local_group_26 0.052 r_gen_planes_other 0.051 r_ncsr_local_group_15 0.051 r_ncsr_local_group_33 0.05 r_ncsr_local_group_36 0.05 r_ncsr_local_group_37 0.05 r_ncsr_local_group_22 0.049 r_ncsr_local_group_35 0.049 r_ncsr_local_group_16 0.047 r_ncsr_local_group_24 0.047 r_ncsr_local_group_13 0.046 r_ncsr_local_group_19 0.046 r_ncsr_local_group_14 0.045 r_ncsr_local_group_2 0.043 r_ncsr_local_group_7 0.043 r_ncsr_local_group_39 0.043 r_ncsr_local_group_5 0.042 r_ncsr_local_group_20 0.041 r_ncsr_local_group_40 0.041 r_ncsr_local_group_3 0.04 r_ncsr_local_group_31 0.04 r_ncsr_local_group_9 0.038 r_ncsr_local_group_10 0.038 r_ncsr_local_group_25 0.033 r_ncsr_local_group_23 0.03 r_ncsr_local_group_34 0.03 r_xyhbond_nbd_other 0.024 r_ncsr_local_group_32 0.024 r_bond_refined_d 0.009 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20629 Nucleic Acid Atoms Solvent Atoms 1339 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing