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S1C 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, HANGING DROP 293 Na cacodylate 50mM pH 5.6
Peg 4000 16% (w/v)
Na thiocyante 0.5 M
NaCl 50 mM
Isoproponal 10% (v/v)
Crystal Properties Matthews coefficient Solvent content 2.27 45.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.26 α = 69.27 b = 96.26 β = 69.27 c = 100.206 γ = 76.77
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 2013-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 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 2.8 40 88.4 0.14 6.6 2.1 68030
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 2.8 2.95 89 0.552 1.9 2.2
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 2.8 38.24 64608 3420 88.38 0.21577 0.21385 0.2162 0.25142 0.2515 RANDOM 48.39
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] 0.3 -1.54 -1.2 -0.48 -0.82 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.397 r_dihedral_angle_3_deg 17.332 r_dihedral_angle_4_deg 16.01 r_long_range_B_refined 8.076 r_long_range_B_other 8.075 r_dihedral_angle_1_deg 6.27 r_scangle_other 5.199 r_mcangle_it 4.66 r_mcangle_other 4.66 r_angle_other_deg 3.663
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.397 r_dihedral_angle_3_deg 17.332 r_dihedral_angle_4_deg 16.01 r_long_range_B_refined 8.076 r_long_range_B_other 8.075 r_dihedral_angle_1_deg 6.27 r_scangle_other 5.199 r_mcangle_it 4.66 r_mcangle_other 4.66 r_angle_other_deg 3.663 r_scbond_it 3.23 r_scbond_other 3.23 r_mcbond_it 2.924 r_mcbond_other 2.924 r_angle_refined_deg 1.403 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 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 23696 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing