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PDX1.2/PDX1.3 complex (PDX1.3:K97A)
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, pH 6.5, 5% 1,4-dioxane, 0.01 M Tris, pH 7.0, 0.1 M KCl, 0.005 M DTT
Crystal Properties Matthews coefficient Solvent content 2.58 52.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.46 α = 90 b = 177.46 β = 90 c = 115.77 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 PILATUS 2M-F 2015-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00002 SLS X06DA
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 2.53 92.47 100 0.177 0.209 0.109 0.991 9 7.2 45389
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 2.53 2.62 100 0.976 1.159 0.616 0.639 2.2 7.1
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 2.53 92.47 43157 2229 99.99 0.2369 0.2347 0.2394 0.2807 0.2442 RANDOM 29.321
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] -2.06 -1.03 -2.06 6.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.919 r_dihedral_angle_4_deg 16.41 r_dihedral_angle_3_deg 15.99 r_dihedral_angle_1_deg 5.195 r_angle_refined_deg 1.059 r_angle_other_deg 0.555 r_chiral_restr 0.052 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.919 r_dihedral_angle_4_deg 16.41 r_dihedral_angle_3_deg 15.99 r_dihedral_angle_1_deg 5.195 r_angle_refined_deg 1.059 r_angle_other_deg 0.555 r_chiral_restr 0.052 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14778 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction Aimless data scaling PHASER phasing