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Crystal structure of Group A Streptococcus HupZ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HTD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% PEG 3350, 0.2M Lithium Acetate
Crystal Properties Matthews coefficient Solvent content 2.53 51.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.823 α = 78.59 b = 61.181 β = 86.76 c = 61.347 γ = 80.07
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 MARMOSAIC 300 mm CCD 2012-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.8 APS 22-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 2 50 98.2 0.099 13.6 3.6 39089
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 2 2.03 97.7 0.377 7.69 3.8
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 2HTD 2 46.88 34858 3898 97.03 0.17078 0.16658 0.1729 0.20803 0.2141 RANDOM 25.664
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] 1.35 -0.33 -0.63 -0.23 0.41 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.065 r_dihedral_angle_4_deg 18.199 r_dihedral_angle_3_deg 16.603 r_long_range_B_refined 7.039 r_long_range_B_other 6.957 r_dihedral_angle_1_deg 6.608 r_scangle_other 5.049 r_scbond_it 3.359 r_scbond_other 3.358 r_mcangle_it 2.996
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.065 r_dihedral_angle_4_deg 18.199 r_dihedral_angle_3_deg 16.603 r_long_range_B_refined 7.039 r_long_range_B_other 6.957 r_dihedral_angle_1_deg 6.608 r_scangle_other 5.049 r_scbond_it 3.359 r_scbond_other 3.358 r_mcangle_it 2.996 r_mcangle_other 2.996 r_angle_refined_deg 2.05 r_mcbond_it 2.014 r_mcbond_other 2.013 r_angle_other_deg 1.114 r_chiral_restr 0.123 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_bond_other_d 0.005 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 3812 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing