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Crystal structure of GPb in complex with DK11
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 2.51 51.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.474 α = 90 b = 128.474 β = 90 c = 116.382 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 2011-10-07 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 2.6 13.9 98.9 0.11 9.7 3.5 30115 30115
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 2.6 2.74 99.3 0.467 1.7 2.3 4338
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 (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 2.6 13.66 28572 1519 99.34 0.158 0.16168 0.15797 0.1548 0.23088 0.2246 RANDOM 26.329
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] 0.01 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.228 r_dihedral_angle_4_deg 21.497 r_dihedral_angle_3_deg 19.12 r_dihedral_angle_1_deg 6.804 r_scangle_it 4.654 r_scbond_it 2.705 r_mcangle_it 1.731 r_angle_refined_deg 1.715 r_mcbond_it 0.877 r_chiral_restr 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.228 r_dihedral_angle_4_deg 21.497 r_dihedral_angle_3_deg 19.12 r_dihedral_angle_1_deg 6.804 r_scangle_it 4.654 r_scbond_it 2.705 r_mcangle_it 1.731 r_angle_refined_deg 1.715 r_mcbond_it 0.877 r_chiral_restr 0.126 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 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 6604 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 26
Software Software Software Name Purpose CrysalisPro data collection REFMAC refinement CrysalisPro data reduction SCALA data scaling