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Spitrobot-2 advances time-resolvedcryo-trapping crystallography to under 25 ms: T4 Lysozyme, mutant L99A bound with indole (1 s soaking)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4W51
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7 293 4 M sodium/potassium phosphate pH 7.0, 0.1 M 1,6-hexanediol, 0.15 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.75 55.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.173 α = 90 b = 60.173 β = 90 c = 97.217 γ = 120
Symmetry Space Group P 32 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 X 16M 2024-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.976 PETRA III, EMBL c/o DESY P14 (MX2)
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 1.896 52.17 87.4 0.992 8.4 18.3 11696
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 1.896 2.008 0.517
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.9 52.17 11148 548 69.98 0.2092 0.20716 0.2133 0.24867 0.2575 RANDOM 24.552
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] -0.39 -0.2 -0.39 1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.672 r_dihedral_angle_2_deg 7.548 r_dihedral_angle_1_deg 6.159 r_long_range_B_refined 5.399 r_long_range_B_other 5.379 r_scangle_other 4.261 r_scbond_it 2.745 r_scbond_other 2.744 r_mcangle_it 2.668 r_mcangle_other 2.668
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.672 r_dihedral_angle_2_deg 7.548 r_dihedral_angle_1_deg 6.159 r_long_range_B_refined 5.399 r_long_range_B_other 5.379 r_scangle_other 4.261 r_scbond_it 2.745 r_scbond_other 2.744 r_mcangle_it 2.668 r_mcangle_other 2.668 r_mcbond_it 1.857 r_mcbond_other 1.856 r_angle_refined_deg 1.785 r_angle_other_deg 0.607 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1290 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 9
Software Software Software Name Purpose XDS data reduction autoPROC data reduction Aimless data scaling autoPROC data scaling PHASER phasing REFMAC refinement