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Streptococcus pyogenes Apo-GapN C284S variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other unpublished
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 0.2 M lithium sulfate
0.1 M Bis-Tris pH 6.5
18 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.03 39.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.665 α = 96.36 b = 126.036 β = 104.81 c = 148.393 γ = 84.23
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 X 2M 2021-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873128 ESRF ID23-2
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 1.499 47.634 89.97 0.122 0.151 0.087 0.9921 5.444 2.76 744804 1.2
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 1.499 1.635 63.75 0.705 0.866 0.497 0.4662 1.569 2.89
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(Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT unpublished 1.5 19.97 744550 18412 68.6 0.2007 0.1999 0.1964 0.2316 0.229 RANDOM 16.85
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] -0.5078 -4.5178 0.7058 3.0068 0.5407 -2.499
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.13 t_omega_torsion 3.74 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 56832 Nucleic Acid Atoms Solvent Atoms 6361 Heterogen Atoms 305
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing