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Crystal structure of GPb in complex with DK16
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SYM PDB entry 3SYM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 6.7 289 10mM BES buffer, pH 6.7, SMALL TUBES, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.52 51.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.586 α = 90 b = 128.586 β = 90 c = 116.428 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD AGILENT ATLAS CCD 2011-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.5419
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.4 13.8 99.4 0.099 17.4 8.5 38517 38517
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 100 0.475 2.7 5.5 5557
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB entry 3SYM 2.4 13.7 36524 36524 1930 99.94 0.163 0.16305 0.16016 0.1578 0.21765 0.2126 RANDOM 24.915
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.54 r_dihedral_angle_4_deg 22.965 r_dihedral_angle_3_deg 18.367 r_dihedral_angle_1_deg 6.669 r_scangle_it 5.861 r_scbond_it 3.556 r_mcangle_it 2.149 r_angle_refined_deg 1.907 r_mcbond_it 1.104 r_chiral_restr 0.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.54 r_dihedral_angle_4_deg 22.965 r_dihedral_angle_3_deg 18.367 r_dihedral_angle_1_deg 6.669 r_scangle_it 5.861 r_scbond_it 3.556 r_mcangle_it 2.149 r_angle_refined_deg 1.907 r_mcbond_it 1.104 r_chiral_restr 0.135 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6605 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 24
Software Software Software Name Purpose CrysalisPro data collection REFMAC refinement CrysalisPro data reduction SCALA data scaling REFMAC phasing