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Spitrobot-2 advances time-resolvedcryo-trapping crystallography to under 25 ms: T4 Lysozyme, mutant L99A (apo state)
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 2.72 54.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.097 α = 90 b = 60.097 β = 90 c = 96.251 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 2024-06-13 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 1.497 52.046 94.5 0.998 12.4 18.52 29721
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 1.497 1.567 0.525
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 1.5 52.1 28277 1443 89.87 0.17771 0.17689 0.1863 0.19356 0.2035 RANDOM 21.567
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] -0.07 -0.03 -0.07 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.988 r_dihedral_angle_2_deg 7.1 r_long_range_B_refined 6.075 r_long_range_B_other 6.004 r_dihedral_angle_1_deg 5.421 r_scangle_other 5.096 r_scbond_it 3.315 r_scbond_other 3.312 r_mcangle_it 2.619 r_mcangle_other 2.619
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.988 r_dihedral_angle_2_deg 7.1 r_long_range_B_refined 6.075 r_long_range_B_other 6.004 r_dihedral_angle_1_deg 5.421 r_scangle_other 5.096 r_scbond_it 3.315 r_scbond_other 3.312 r_mcangle_it 2.619 r_mcangle_other 2.619 r_angle_refined_deg 1.823 r_mcbond_it 1.812 r_mcbond_other 1.81 r_angle_other_deg 0.648 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 1295 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction autoPROC data reduction Aimless data scaling autoPROC data scaling PHASER phasing REFMAC refinement