☰ Navigation Tabs
Crystal Structure of Periplasmic glucose binding protein ppGBP deletion mutant- Del-ppGBP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DVI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 0.1 M Bis-Tris, pH 6.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.12 42.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.2 α = 90 b = 137.6 β = 109.5 c = 54.2 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2016-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.5 40 95.4 0.98 6.16 3.64 25721
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 2.5 3 89.9 0.75 3.74
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 5DVI 2.5 37.22 24421 1299 99.39 0.21577 0.21312 0.2659 0.2609 RANDOM 32.152
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] -15.17 -12.43 31.5 -16.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.707 r_dihedral_angle_3_deg 19.284 r_dihedral_angle_4_deg 18.545 r_dihedral_angle_1_deg 7.251 r_long_range_B_refined 6.604 r_long_range_B_other 6.601 r_mcangle_it 2.841 r_mcangle_other 2.841 r_scangle_other 2.218 r_angle_refined_deg 1.787
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.707 r_dihedral_angle_3_deg 19.284 r_dihedral_angle_4_deg 18.545 r_dihedral_angle_1_deg 7.251 r_long_range_B_refined 6.604 r_long_range_B_other 6.601 r_mcangle_it 2.841 r_mcangle_other 2.841 r_scangle_other 2.218 r_angle_refined_deg 1.787 r_mcbond_it 1.738 r_mcbond_other 1.735 r_scbond_it 1.34 r_scbond_other 1.34 r_angle_other_deg 1.123 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5864 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing