☰ Navigation Tabs
Crystal Structure of S1G mutant of Penicillin G Acylase from Kluyvera citrophila
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E3A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 30%(w/v) PEG 4000,
50 mM sodium cacodylate pH 5.6
0.5 M potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.24 45.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54 α = 104.05 b = 124.561 β = 101.37 c = 135.139 γ = 96.51
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M 2012-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.956 SSRL BL12-2
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 2.5 38.6 76.5 0.095 6.1 1.7 87317
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 2.5 2.6 80.6 0.55 1.2 1.6
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 1E3A 2.5 38 82837 4354 76.34 0.25043 0.24823 0.2507 0.29182 0.2902 RANDOM 44.01
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] -2.53 2.76 -0.35 4.17 2.33 -2.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.255 r_dihedral_angle_3_deg 17.614 r_dihedral_angle_4_deg 17.268 r_long_range_B_refined 7.196 r_long_range_B_other 7.183 r_dihedral_angle_1_deg 6.007 r_mcangle_it 4.627 r_mcangle_other 4.627 r_scangle_other 4.618 r_angle_other_deg 3.672
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.255 r_dihedral_angle_3_deg 17.614 r_dihedral_angle_4_deg 17.268 r_long_range_B_refined 7.196 r_long_range_B_other 7.183 r_dihedral_angle_1_deg 6.007 r_mcangle_it 4.627 r_mcangle_other 4.627 r_scangle_other 4.618 r_angle_other_deg 3.672 r_mcbond_it 3.035 r_mcbond_other 3.035 r_scbond_it 3.003 r_scbond_other 3.002 r_angle_refined_deg 1.221 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_other 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25688 Nucleic Acid Atoms Solvent Atoms 428 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing XDS data scaling