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Penicillin Acylase, mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PNK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 277 MOPS buffer, PEG MME 2k, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.15 42.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.586 α = 72.61 b = 63.965 β = 74.09 c = 64.02 γ = 73.68
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 IMAGE PLATE MAC Science DIP-2020 mirrors M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.5418
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 2.28 30 95.7 0.068 9.6 6.4 32764 31355 -3 24.2
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) 2.28 2.3 93.6 0.163 3.9
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1PNK 2.28 29.88 29743 1612 100 0.16873 0.16581 0.22278 RANDOM 19.844
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] 0.05 0.19 -0.27 0.03 -0.24 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.063 r_scangle_it 3.173 r_dihedral_angle_1_deg 3.146 r_scbond_it 1.982 r_angle_refined_deg 1.329 r_mcangle_it 1.122 r_mcbond_it 0.597 r_symmetry_vdw_refined 0.238 r_nbd_refined 0.229 r_symmetry_hbond_refined 0.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.063 r_scangle_it 3.173 r_dihedral_angle_1_deg 3.146 r_scbond_it 1.982 r_angle_refined_deg 1.329 r_mcangle_it 1.122 r_mcbond_it 0.597 r_symmetry_vdw_refined 0.238 r_nbd_refined 0.229 r_symmetry_hbond_refined 0.204 r_xyhbond_nbd_refined 0.145 r_metal_ion_refined 0.112 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6067 Nucleic Acid Atoms Solvent Atoms 416 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling CNS refinement DENZO data reduction CNS phasing