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Crystal structure of protein SPy2152 from Streptococcus pyogenes
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 290 20 % PEG 8000,
Mes pH 6.0,
Ca(OAc)2
, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 1.65 25.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.087 α = 90 b = 30.28 β = 113.26 c = 35.855 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 2005-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97907 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 2.01 50 91.1 0.087 30.26 6.6 5139 4682 -3
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 2.01 2.03 58.6 0.283 3.62 4.1 75
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.15 34.94 3855 3855 185 96.05 0.1611 0.16111 0.15732 0.25389 0.2597 RANDOM 35.876
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] 3.81 -0.16 -2.12 -1.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.803 r_dihedral_angle_3_deg 16.81 r_dihedral_angle_4_deg 14.406 r_dihedral_angle_1_deg 6.349 r_scangle_it 4.323 r_scbond_it 2.888 r_angle_refined_deg 1.813 r_mcangle_it 1.538 r_mcbond_it 0.95 r_symmetry_vdw_refined 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.803 r_dihedral_angle_3_deg 16.81 r_dihedral_angle_4_deg 14.406 r_dihedral_angle_1_deg 6.349 r_scangle_it 4.323 r_scbond_it 2.888 r_angle_refined_deg 1.813 r_mcangle_it 1.538 r_mcbond_it 0.95 r_symmetry_vdw_refined 0.33 r_nbtor_refined 0.319 r_symmetry_hbond_refined 0.272 r_nbd_refined 0.235 r_xyhbond_nbd_refined 0.221 r_chiral_restr 0.102 r_bond_refined_d 0.026 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 627 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling HKL-3000 phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building