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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 2.68 53.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.03 α = 90 b = 93.25 β = 94.21 c = 108.16 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 2004-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 2.4 20 99.8 0.15 9.6 3.7 81439
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 2.4 2.53 100 0.59 2.5 3.7
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 1W79 2.4 16.03 77111 4073 99.9 0.199 0.196 0.1962 0.248 0.2472 RANDOM 28.89
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 -0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.016 r_dihedral_angle_3_deg 17.682 r_dihedral_angle_4_deg 17.214 r_dihedral_angle_1_deg 6.765 r_scangle_it 2.741 r_scbond_it 1.73 r_angle_refined_deg 1.625 r_mcangle_it 1.183 r_mcbond_it 0.678 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.016 r_dihedral_angle_3_deg 17.682 r_dihedral_angle_4_deg 17.214 r_dihedral_angle_1_deg 6.765 r_scangle_it 2.741 r_scbond_it 1.73 r_angle_refined_deg 1.625 r_mcangle_it 1.183 r_mcbond_it 0.678 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.235 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.172 r_symmetry_hbond_refined 0.137 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 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 520 Heterogen Atoms 182
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling