☰ Navigation Tabs
Crystal structure of pneumococcal LicA in complex with choline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4R77
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 0.1M HEPES, 1.2M sodium citrate, 4% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.36 47.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.386 α = 90 b = 96.69 β = 90 c = 98.595 γ = 90
Symmetry Space Group P 21 21 21
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 315r 2013-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97924 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.01 50 98.2 44656 44656 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.08 98 0.571 0.571 3.362 3.4
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 4R77 2.01 29.78 42212 2255 97.94 0.20231 0.20049 0.2052 0.23738 0.2429 RANDOM 36.236
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] 2.82 -2.8 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.624 r_dihedral_angle_4_deg 17.131 r_dihedral_angle_3_deg 14.888 r_dihedral_angle_1_deg 5.382 r_scangle_it 3.091 r_scbond_it 1.811 r_mcangle_it 1.158 r_angle_refined_deg 1.138 r_mcbond_it 0.586 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.624 r_dihedral_angle_4_deg 17.131 r_dihedral_angle_3_deg 14.888 r_dihedral_angle_1_deg 5.382 r_scangle_it 3.091 r_scbond_it 1.811 r_mcangle_it 1.158 r_angle_refined_deg 1.138 r_mcbond_it 0.586 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4678 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 14
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALA data scaling