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Crystal structure of Streptococcal asymmetric Ap4A hydrolase and phosphodiesterase Spr1479/SapH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 25% iso-propanol, 0.1M HEPES, pH 7.5, 0.2M NH4Ac, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.51 51.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.559 α = 90 b = 75.102 β = 90 c = 148.796 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 RAYONIX MX-225 2010-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97885 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 30 99.4 0.082 0.082 21.8 6.7 50589 -3 25.4
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 1.9 1.97 94.9 0.395 0.395 3.8 5.6 4756
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.9 30 47758 2558 98.91 0.19633 0.19458 0.1943 0.22891 0.2278 RANDOM 25.449
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] 2.2 -1.19 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.614 r_dihedral_angle_4_deg 18.667 r_dihedral_angle_3_deg 13.401 r_dihedral_angle_1_deg 5.675 r_scangle_it 3.673 r_scbond_it 2.234 r_mcangle_it 1.359 r_angle_refined_deg 1.309 r_mcbond_it 0.732 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.614 r_dihedral_angle_4_deg 18.667 r_dihedral_angle_3_deg 13.401 r_dihedral_angle_1_deg 5.675 r_scangle_it 3.673 r_scbond_it 2.234 r_mcangle_it 1.359 r_angle_refined_deg 1.309 r_mcbond_it 0.732 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4140 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 4
Software Software Software Name Purpose MAR345dtb data collection SOLVE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling