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Crystal structure of Actinomadura R39 DD-peptidase complexed with a peptidoglycan-mimetic cephalosporin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W79 PDB ENTRY 1W79
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 pH 8
Crystal Properties Matthews coefficient Solvent content 2.71 54.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.14 α = 90 b = 93.35 β = 94.98 c = 109.1 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE MARRESEARCH MIRRORS 2004-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 2.25 20 99.1 0.17 9.7 3.7 99513
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 2.25 2.37 94.9 0.71 2.3 3.5
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 1W79 2.25 15.71 94249 4989 99.2 0.233 0.23 0.2329 0.286 0.234 RANDOM 26.41
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.4 r_dihedral_angle_3_deg 16.694 r_dihedral_angle_4_deg 16.5 r_dihedral_angle_1_deg 5.884 r_scangle_it 1.669 r_angle_refined_deg 1.279 r_scbond_it 1.04 r_mcangle_it 0.736 r_mcbond_it 0.436 r_nbtor_refined 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.4 r_dihedral_angle_3_deg 16.694 r_dihedral_angle_4_deg 16.5 r_dihedral_angle_1_deg 5.884 r_scangle_it 1.669 r_angle_refined_deg 1.279 r_scbond_it 1.04 r_mcangle_it 0.736 r_mcbond_it 0.436 r_nbtor_refined 0.292 r_symmetry_vdw_refined 0.23 r_nbd_refined 0.184 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 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 13394 Nucleic Acid Atoms Solvent Atoms 495 Heterogen Atoms 155
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling