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Crystal structure of GacS D1 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MMN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.2 M to 1.2 M Na acetate and 0.1 M HEPES from pH 7 to pH 8 in presence of 50 mM cadmium sulfate
Crystal Properties Matthews coefficient Solvent content 1.92 35.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.152 α = 90 b = 73.532 β = 90 c = 104.348 γ = 90
Symmetry Space Group C 2 2 21
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 EIGER X 9M 2017-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 1.033 SOLEIL PROXIMA 2
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 1.45 36.79 100 0.99 11 8 47424
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 1.45 1.47 0.63
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3MMN 1.45 36.79 45083 2306 99.9 0.1321 0.131 0.1535 0.175 RANDOM 19.983
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] -0.75 0.6 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.971 r_dihedral_angle_4_deg 19.994 r_dihedral_angle_3_deg 11.74 r_dihedral_angle_1_deg 6.18 r_rigid_bond_restr 2.746 r_angle_refined_deg 1.563 r_angle_other_deg 1.51 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.971 r_dihedral_angle_4_deg 19.994 r_dihedral_angle_3_deg 11.74 r_dihedral_angle_1_deg 6.18 r_rigid_bond_restr 2.746 r_angle_refined_deg 1.563 r_angle_other_deg 1.51 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2009 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing