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Nanobody (NbLumSyt1) bound to human Syt1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6I2G 6I2G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 1.6 M DL-malic acid
Crystal Properties Matthews coefficient Solvent content 2.95 58.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.955 α = 90 b = 100.226 β = 100.832 c = 103.939 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 EIGER2 XE 16M 2022-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.976 Diamond I04
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 2.75 60.57 100 0.998 10.3 6.7 46246
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 2.75 2.85 0.898
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 6I2G 2.75 59.11 46155 2370 99.792 0.265 0.2634 0.2826 0.2977 0.3032 94.158
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] -8.932 -0.921 -9.965 17.937
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.197 r_lrange_other 15.493 r_lrange_it 15.489 r_dihedral_angle_6_deg 14.478 r_scangle_other 12.062 r_scangle_it 12.061 r_mcangle_it 12.046 r_mcangle_other 12.045 r_mcbond_it 8.019 r_mcbond_other 8.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.197 r_lrange_other 15.493 r_lrange_it 15.489 r_dihedral_angle_6_deg 14.478 r_scangle_other 12.062 r_scangle_it 12.061 r_mcangle_it 12.046 r_mcangle_other 12.045 r_mcbond_it 8.019 r_mcbond_other 8.014 r_scbond_it 7.834 r_scbond_other 7.833 r_dihedral_angle_2_deg 7.146 r_dihedral_angle_1_deg 6.412 r_angle_refined_deg 1.185 r_angle_other_deg 0.449 r_nbd_refined 0.205 r_symmetry_nbd_other 0.203 r_xyhbond_nbd_refined 0.193 r_nbtor_refined 0.174 r_nbd_other 0.168 r_ncsr_local_group_29 0.16 r_ncsr_local_group_54 0.154 r_ncsr_local_group_45 0.143 r_ncsr_local_group_34 0.142 r_ncsr_local_group_40 0.142 r_ncsr_local_group_49 0.135 r_ncsr_local_group_52 0.133 r_ncsr_local_group_44 0.129 r_ncsr_local_group_36 0.127 r_ncsr_local_group_30 0.121 r_symmetry_nbd_refined 0.114 r_ncsr_local_group_32 0.108 r_ncsr_local_group_56 0.103 r_ncsr_local_group_20 0.102 r_ncsr_local_group_42 0.101 r_ncsr_local_group_33 0.097 r_ncsr_local_group_48 0.097 r_ncsr_local_group_6 0.096 r_ncsr_local_group_26 0.096 r_ncsr_local_group_16 0.095 r_ncsr_local_group_21 0.094 r_ncsr_local_group_19 0.092 r_ncsr_local_group_46 0.092 r_ncsr_local_group_12 0.091 r_ncsr_local_group_17 0.091 r_ncsr_local_group_39 0.091 r_ncsr_local_group_15 0.088 r_ncsr_local_group_5 0.087 r_ncsr_local_group_11 0.087 r_ncsr_local_group_28 0.087 r_ncsr_local_group_24 0.086 r_ncsr_local_group_22 0.085 r_ncsr_local_group_37 0.085 r_ncsr_local_group_7 0.084 r_ncsr_local_group_51 0.084 r_ncsr_local_group_38 0.083 r_ncsr_local_group_4 0.082 r_symmetry_nbtor_other 0.081 r_ncsr_local_group_55 0.081 r_ncsr_local_group_18 0.079 r_ncsr_local_group_27 0.079 r_ncsr_local_group_53 0.079 r_ncsr_local_group_2 0.078 r_ncsr_local_group_3 0.078 r_ncsr_local_group_13 0.078 r_ncsr_local_group_50 0.078 r_ncsr_local_group_10 0.076 r_symmetry_xyhbond_nbd_other 0.074 r_ncsr_local_group_1 0.069 r_ncsr_local_group_23 0.068 r_ncsr_local_group_14 0.067 r_ncsr_local_group_9 0.065 r_ncsr_local_group_25 0.064 r_ncsr_local_group_31 0.061 r_chiral_restr 0.06 r_ncsr_local_group_8 0.059 r_ncsr_local_group_47 0.058 r_ncsr_local_group_43 0.042 r_ncsr_local_group_41 0.028 r_ncsr_local_group_35 0.027 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7705 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing