☰ Navigation Tabs
Crystal structure of Zn(II)-bound ZinT-like domain of Streptococcus pneumoniae AdcA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OEK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 0.1 M sodium acetate, pH 4.5,
30 % (w/v) PEG MME 5000
Crystal Properties Matthews coefficient Solvent content 2.31 46.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.251 α = 90 b = 50.091 β = 90 c = 87.215 γ = 90
Symmetry Space Group P 21 2 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 210r 2014-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.954 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.1 19.72 100 0.03 0.99 13.2 2 79405 9.30931181088
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.14 0.29 0.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1OEK 1.1 19.72 1.33414552556 79404 3917 99.9949627242 0.147950940525 0.146947165944 0.1481 0.167280499897 0.1678 16.3663010563
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 f_dihedral_angle_d 15.9927611443 f_angle_d 0.896224821257 f_chiral_restr 0.0732753374994 f_bond_d 0.00651402302853 f_plane_restr 0.00625984275128
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1465 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 9
Software Software Software Name Purpose PHENIX refinement XDS data scaling PHASER phasing PHENIX model building