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Crystal structure of the Zn(II)-bound ZnuA-like domain of Streptococcus pneumoniae AdcA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OSV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 12.5% (w/v) polyethylene glycol 1000,
12.5% (w/v) PEG 3350,
12.5% (v/v) 2-methyl-2,4-pentanediol,
0.03 M MgCl2,
0.03 M CaCl2,
0.1 M imidazole-MES, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.11 41.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.372 α = 92.275 b = 67.956 β = 104.697 c = 79.622 γ = 115.959
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 2015-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.954 Australian Synchrotron MX1
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 2.03 19.36 98.2 0.108 0.99 8.6 3.9 68710 28.9744951541
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 2.03 2.1 0.804 0.66
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 2OSV 2.03 19.36 1.89478673062 68697 1999 98.1582030692 0.170294108042 0.169005718258 0.1695 0.212820796565 0.2127 36.10957472
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 16.5678150831 f_angle_d 0.97873154662 f_chiral_restr 0.0567272303075 f_bond_d 0.00740561200463 f_plane_restr 0.00651031407842
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8352 Nucleic Acid Atoms Solvent Atoms 462 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement XDS data scaling PHASER phasing PHENIX model building