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Covalent Penicilloyl Acyl Enzyme Complex Of The Streptomyces R61 DD-Peptidase With A Highly Specific Penicillin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PTE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 20% PEG 8000, 50mM Sodium Phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 1.95 45.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.9 α = 90 b = 66.7 β = 90 c = 100.2 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 MIRRORS 2002-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 1.00 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 1.074 50 95.9 0.07 24.6 6.4 147076 141081 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 1.074 1.12 72.5 0.068 9.9 1.9 10531
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R 3PTE 1.074 10 132892 132892 7081 89.5 0.1106 0.1106 0.1059 0.1147 0.1458 0.1311 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 22 542 3156.03
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.094 s_approx_iso_adps 0.092 s_zero_chiral_vol 0.087 s_anti_bump_dis_restr 0.057 s_from_restr_planes 0.0325 s_similar_adp_cmpnt 0.032 s_bond_d 0.03 s_angle_d 0.03 s_rigid_bond_adp_cmpnt 0.006 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2602 Nucleic Acid Atoms Solvent Atoms 550 Heterogen Atoms 29
Software Software Software Name Purpose SHELXL-97 refinement SCALEPACK data scaling CNS refinement DENZO data reduction CNS phasing