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Wild-type Bacillus megaterium Penicillin G Acylase with Covalently Bound Phenylacetic Acid
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PNM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 1 mM Penicillin G, 0.150 M NaCl, 31% w/v PEG 4000, and 0.1 M imidazole (pH 6.5)
Crystal Properties Matthews coefficient Solvent content 2.2 43.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.811 α = 90 b = 78.056 β = 101.537 c = 85.347 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 CCD ADSC QUANTUM 315 2007-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 0.99998 NSRRC BL13B1
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
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 1.71 30 97.5 0.043 23.45 3.5 80619 15.95
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 1.71 1.77 81.8 0.183 5.66 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1PNM 1.71 28.67 1.36 78547 3947 97.22 0.1367 0.1355 0.1358 0.1582 0.1585 23.72
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.0635 f_angle_d 0.8418 f_chiral_restr 0.0507 f_bond_d 0.0068 f_plane_restr 0.0066
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5889 Nucleic Acid Atoms Solvent Atoms 1407 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing