☰ Navigation Tabs
The Crystal Structure of a protein in the NADB-Rossmann Superfamily from Streptococcus agalactiae to 1.8A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GNL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 289 2M Ammonium sulfate, 0.1M Tris pH 7.0, 0.2M Lithium sulfate, vapor diffusion, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.04 39.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.444 α = 90 b = 62.871 β = 107.77 c = 61.784 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315 2009-03-19 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.8 50 99.7 0.084 9.3 3.1 19085
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 99.9 0.551 3.1
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 THROUGHOUT 3GNL 1.8 37.93 19083 979 99.2 0.209 0.207 0.2073 0.248 0.2483 RANDOM 23.95
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] -0.18 0.07 0.41 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.819 r_dihedral_angle_3_deg 14.439 r_dihedral_angle_4_deg 11.882 r_dihedral_angle_1_deg 5.471 r_scangle_it 3.663 r_scbond_it 2.363 r_angle_refined_deg 1.306 r_mcangle_it 1.293 r_mcbond_it 0.711 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.819 r_dihedral_angle_3_deg 14.439 r_dihedral_angle_4_deg 11.882 r_dihedral_angle_1_deg 5.471 r_scangle_it 3.663 r_scbond_it 2.363 r_angle_refined_deg 1.306 r_mcangle_it 1.293 r_mcbond_it 0.711 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 1755 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 16
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection PHASER phasing