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Crystal structure of a M20 family metallo peptidase from Streptococcus pneumoniae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 295 0.2M Ammonium acetate, 0.5M Sodium chloride, 20% w/v PEG 3350, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.44 49.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.954 α = 90 b = 101.922 β = 90 c = 118.074 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 MARMOSAIC 300 mm CCD mirrors 2006-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0000 APS 23-ID-D
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 1.9 25 99.6 0.062 17.1 3.7 83179 83179 -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 1.9 1.97 100 0.367 2.9 3.7 8229
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 MIRAS THROUGHOUT 1.9 25 79025 4150 99.42 0.18053 0.1781 0.1781 0.22579 0.2261 RANDOM 28.493
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] -2.86 -1.66 4.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.26 r_dihedral_angle_4_deg 15.662 r_dihedral_angle_3_deg 12.401 r_scangle_it 5.081 r_dihedral_angle_1_deg 4.784 r_scbond_it 3.222 r_mcangle_it 1.94 r_angle_refined_deg 1.555 r_mcbond_it 1.289 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.26 r_dihedral_angle_4_deg 15.662 r_dihedral_angle_3_deg 12.401 r_scangle_it 5.081 r_dihedral_angle_1_deg 4.784 r_scbond_it 3.222 r_mcangle_it 1.94 r_angle_refined_deg 1.555 r_mcbond_it 1.289 r_nbtor_refined 0.321 r_xyhbond_nbd_refined 0.223 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.21 r_symmetry_hbond_refined 0.202 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7261 Nucleic Acid Atoms Solvent Atoms 817 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling SHARP phasing