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CRYSTAL STRUCTURE OF STREPTOMYCES R61 DD-PEPTIDASE COMPLEXED WITH A NOVEL CEPHALOSPORIN ANALOG OF CELL WALL PEPTIDOGLYCAN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PTE PDB ENTRY 3PTE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 PEG 8000, sodium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.94 36.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.778 α = 90 b = 66.664 β = 90 c = 100.928 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 BRANDEIS - B4 Monochromator, Mirror 2000-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 0.9790 NSLS X12C
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 1.17 20 95.9 0.04 25 5 2330719 111370 18.6
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 1.17 1.21 72.9 0.162 4.6 8392
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS free r PDB ENTRY 3PTE 1.17 10 111197 111197 5560 96.1 0.1141 0.1141 0.1126 0.1528 RANDOM 16.1
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 35 268.92 3181.8
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.102 s_non_zero_chiral_vol 0.091 s_zero_chiral_vol 0.082 s_similar_adp_cmpnt 0.041 s_from_restr_planes 0.0311 s_angle_d 0.03 s_anti_bump_dis_restr 0.026 s_bond_d 0.014 s_rigid_bond_adp_cmpnt 0.006 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2607 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 51
Software Software Software Name Purpose SHELXL-97 refinement SCALEPACK data scaling CNS refinement DENZO data reduction CNS phasing