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Streptococcus pyogenes apo GapN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EUH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293.15 0.2 M Lithium sulfate
0.1 M Bis-Tris pH 5.5
25 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.12 42.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.749 α = 77.67 b = 99.893 β = 75.19 c = 106.182 γ = 67.12
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 PILATUS3 6M 2020-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.918401 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.989 48.148 87.49 0.304 0.373 0.213 0.8467 3.195 2.91 153369 1.2 22.25
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.989 2.17 70.72 1.002 1.201 0.655 0.3963 3.23
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 (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 1EUH 1.989 20.03 153157 7387 62.9 0.1942 0.1923 0.1855 0.2319 0.2234 RANDOM 24.99
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] -2.2365 -1.0871 1.8202 -0.7198 2.7898 2.9564
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.77 t_omega_torsion 3.35 t_angle_deg 1.01 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_sum_occupancies t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28376 Nucleic Acid Atoms Solvent Atoms 2243 Heterogen Atoms 272
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing