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Crystal structure of 23ME-00610 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other FAB core
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 MPD 50.0% v/v; NH4H2PO4 0.20M; Tris-HCL 0.10M pH 8.50
Crystal Properties Matthews coefficient Solvent content 2.6 52.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 225.274 α = 90 b = 67.447 β = 101.71 c = 136.88 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 EIGER2 S 16M 2022-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.12 95.167 97.8 0.159 0.989 7.8 7.4 112044
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.157 1.178 0.46
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 2.12 67.106 111756 5592 97.543 0.22 0.2182 0.2221 0.2562 0.2616 43.299
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] 3.704 -2.166 -1.222 -1.459
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.298 r_dihedral_angle_4_deg 18.149 r_dihedral_angle_3_deg 12.995 r_dihedral_angle_1_deg 7.572 r_lrange_it 5.634 r_lrange_other 5.598 r_scangle_it 3.26 r_scangle_other 3.26 r_mcangle_it 3.174 r_mcangle_other 3.174
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.298 r_dihedral_angle_4_deg 18.149 r_dihedral_angle_3_deg 12.995 r_dihedral_angle_1_deg 7.572 r_lrange_it 5.634 r_lrange_other 5.598 r_scangle_it 3.26 r_scangle_other 3.26 r_mcangle_it 3.174 r_mcangle_other 3.174 r_scbond_it 2.022 r_scbond_other 2.022 r_mcbond_it 1.967 r_mcbond_other 1.967 r_angle_refined_deg 1.391 r_angle_other_deg 1.105 r_ext_dist_refined_d 0.599 r_symmetry_nbd_other 0.151 r_nbd_other 0.151 r_nbd_refined 0.147 r_nbtor_refined 0.141 r_xyhbond_nbd_refined 0.135 r_symmetry_xyhbond_nbd_refined 0.13 r_symmetry_nbd_refined 0.075 r_symmetry_nbtor_other 0.067 r_chiral_restr 0.048 r_ncsr_local_group_8 0.031 r_ncsr_local_group_2 0.03 r_ncsr_local_group_11 0.03 r_ncsr_local_group_1 0.027 r_ncsr_local_group_7 0.025 r_ncsr_local_group_3 0.023 r_ncsr_local_group_4 0.019 r_ncsr_local_group_6 0.019 r_ncsr_local_group_9 0.017 r_ncsr_local_group_5 0.015 r_ncsr_local_group_10 0.015 r_ncsr_local_group_12 0.015 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13091 Nucleic Acid Atoms Solvent Atoms 749 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing