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Acid phosphatase KpAP mutant - E104G
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 300 0.2 M Ammonium acetate, 0.1 M BIS-TRIS, 45% (v/v) (+/-)-2-Methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 4.31 71.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.71 α = 90 b = 124.71 β = 90 c = 97.28 γ = 120
Symmetry Space Group P 63 2 2
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 DECTRIS PILATUS 6M 2024-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.987 SSRF BL19U1
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 1.93 47.21 100 0.192 15.8 30.3 34115
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 1.97 1.8 0.503
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.93 47.21 32342 1765 99.89 0.17917 0.17817 0.1872 0.19772 0.2072 RANDOM 33.159
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] 0.77 0.39 0.77 -2.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.916 r_dihedral_angle_4_deg 18.639 r_dihedral_angle_3_deg 11.744 r_long_range_B_refined 7.456 r_long_range_B_other 7.001 r_dihedral_angle_1_deg 4.778 r_angle_refined_deg 1.589 r_mcangle_it 0.791 r_mcangle_other 0.79 r_scangle_other 0.705
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.916 r_dihedral_angle_4_deg 18.639 r_dihedral_angle_3_deg 11.744 r_long_range_B_refined 7.456 r_long_range_B_other 7.001 r_dihedral_angle_1_deg 4.778 r_angle_refined_deg 1.589 r_mcangle_it 0.791 r_mcangle_other 0.79 r_scangle_other 0.705 r_angle_other_deg 0.684 r_scbond_it 0.493 r_scbond_other 0.492 r_mcbond_other 0.431 r_mcbond_it 0.43 r_chiral_restr 0.05 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 1772 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 53
Software Software Software Name Purpose HKL-3000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing