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Structure of Streptococcus pneumoniae peptidoglycan deacetylase (SpPgdA) D 275 N Mutant.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C1G PDB ENTRY 2C1G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 PROTEIN WAS CRYSTALLIZED FROM 35% PEG 200, 5% PEG 3000, 100 MM MES, PH 6; THEN SOAKED IN 10 MM ZNCL2. FOLLOWED BY SOAK IN 20%PEG 200, 100MM MES, PH 6
Crystal Properties Matthews coefficient Solvent content 2.2 43.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.275 α = 90 b = 79.239 β = 90 c = 100.377 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 MARRESEARCH MIRROR 2004-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 1.35 15 94.3 0.07 16.8 5.4 93309 2
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 1.35 1.4 94.5 0.44 2.8 2.7
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 PDB ENTRY 2C1G 1.35 15 91377 1840 94.2 0.189 0.188 0.2093 0.225 0.2455 RANDOM 20.78
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] 0.44 -0.02 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.858 r_dihedral_angle_4_deg 18.787 r_dihedral_angle_3_deg 14.448 r_dihedral_angle_1_deg 6.493 r_scangle_it 4.478 r_scbond_it 3.345 r_mcangle_it 2.366 r_mcbond_it 1.697 r_angle_refined_deg 1.569 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.858 r_dihedral_angle_4_deg 18.787 r_dihedral_angle_3_deg 14.448 r_dihedral_angle_1_deg 6.493 r_scangle_it 4.478 r_scbond_it 3.345 r_mcangle_it 2.366 r_mcbond_it 1.697 r_angle_refined_deg 1.569 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.228 r_nbd_refined 0.216 r_symmetry_hbond_refined 0.132 r_chiral_restr 0.105 r_xyhbond_nbd_refined 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3085 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement HKL data reduction HKL data scaling