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Crystal structure of PepS from Streptococcus pneumoniae in complex with a substrate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 2M MAGNESIUM SULFATE, PH 4.6, MICROBATCH, TEMPERATURE 295K
Crystal Properties Matthews coefficient Solvent content 3.07 59.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.365 α = 90 b = 126.365 β = 90 c = 139.328 γ = 90
Symmetry Space Group P 43 21 2
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 BRUKER PROTEUM 300 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 6B PAL/PLS 6B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.97 50 99.6 0.083 42.06 9.3 75799
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.02 100 0.424 5.07 8.4
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 MOLECULAR REPLACEMENT THROUGHOUT 1.97 41.2 75795 4012 99.6 0.227 0.225 0.2147 0.257 0.2451 RANDOM 29.58
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] -0.06 -0.06 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.134 r_dihedral_angle_4_deg 21.441 r_dihedral_angle_3_deg 16.853 r_dihedral_angle_1_deg 6.55 r_scangle_it 4.769 r_scbond_it 3.066 r_angle_refined_deg 1.762 r_mcangle_it 1.655 r_mcbond_it 0.93 r_chiral_restr 0.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.134 r_dihedral_angle_4_deg 21.441 r_dihedral_angle_3_deg 16.853 r_dihedral_angle_1_deg 6.55 r_scangle_it 4.769 r_scbond_it 3.066 r_angle_refined_deg 1.762 r_mcangle_it 1.655 r_mcbond_it 0.93 r_chiral_restr 0.142 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 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 6364 Nucleic Acid Atoms Solvent Atoms 512 Heterogen Atoms 42
Software Software Software Name Purpose EPMR phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling