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PDX1.2/PDX1.3 complex (intermediate)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K3V Chainsaw model derived from 5K3V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 0.8 M ammonium sulphate, 0.05 M MES.OH, pH 6.5, 5% 1,4-dioxane, 0.013 M ammonium sulphate, 0.003 M R5P, 0.001 M G3P, 0.02 M Tris.HCl, pH 8.0, 0.1 M KCl, 0.005 M DTT
Crystal Properties Matthews coefficient Solvent content 2.62 53.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.976 α = 90 b = 177.976 β = 90 c = 116.855 γ = 120
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 S 6M 2015-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.97853 SLS X06SA
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 1.84 93.12 99.4 0.126 0.149 0.087 0.997 8.1 6.8 119464
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 1.84 1.87 97.4 2.143 2.639 1.502 0.085 0.9 5.2
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 Chainsaw model derived from 5K3V 1.9 93.12 102475 5782 99.53 0.2171 0.2163 0.2219 0.2314 0.2172 RANDOM 29.775
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] -1.27 -0.64 -1.27 4.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.992 r_dihedral_angle_4_deg 14.786 r_dihedral_angle_3_deg 12.892 r_dihedral_angle_1_deg 4.439 r_angle_refined_deg 0.687 r_angle_other_deg 0.5 r_chiral_restr 0.04 r_bond_refined_d 0.003 r_gen_planes_refined 0.002 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.992 r_dihedral_angle_4_deg 14.786 r_dihedral_angle_3_deg 12.892 r_dihedral_angle_1_deg 4.439 r_angle_refined_deg 0.687 r_angle_other_deg 0.5 r_chiral_restr 0.04 r_bond_refined_d 0.003 r_gen_planes_refined 0.002 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14726 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction Aimless data scaling PHASER phasing