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COMPLEX OF STREPTOMYCES R61 DD-PEPTIDASE WITH THE PRODUCTS OF A SPECIFIC PEPTIDOGLYCAN SUBSTRATE FRAGMENT
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 6.8 293 PEG 8000, SODIUM PHOSPHATE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal Properties Matthews coefficient Solvent content 1.97 37.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.859 α = 90 b = 66.799 β = 90 c = 100.263 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, MIRRORS 2000-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C NSLS X12C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.25 20 96.7 0.069 17.2 5.6 95204 92030 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.29 77.8 0.178 2 2 7323
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R PDB ENTRY 3PTE 1.25 10 89053 84590 4463 89.1 0.1094 0.1112 0.154 RANDOM
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 26 3215
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.1 s_non_zero_chiral_vol 0.08 s_zero_chiral_vol 0.07 s_from_restr_planes 0.032 s_similar_adp_cmpnt 0.03 s_angle_d 0.02 s_anti_bump_dis_restr 0.02 s_bond_d 0.01 s_similar_dist s_rigid_bond_adp_cmpnt
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2602 Nucleic Acid Atoms Solvent Atoms 587 Heterogen Atoms 27
Software Software Software Name Purpose SHELXL-97 refinement SCALEPACK data scaling CNS refinement DENZO data reduction CNS phasing