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Crystal structure of Ornithine decarboxylase H216F mutant without PLP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ORD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2M Ammonium tartrate dibasic, pH 6.6, 10% v/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.27 45.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.012 α = 107.19 b = 73.12 β = 114.42 c = 78.782 γ = 100.24
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 EIGER2 S 9M 2023-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97933 PAL/PLS 7A (6B, 6C1)
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 2.64 46.79 97.7 0.111 8.1 3.6 36106
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 2.64 2.79 0.203
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 2.64 44.54 36106 1917 97.66 0.17201 0.16846 0.1806 0.24186 0.2466 RANDOM 43.346
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] 0.07 0.15 -0.05 -0.08 0.06 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.962 r_dihedral_angle_3_deg 17.975 r_long_range_B_other 8.574 r_long_range_B_refined 8.573 r_dihedral_angle_1_deg 7.377 r_scangle_other 6.547 r_mcangle_it 5.351 r_mcangle_other 5.351 r_scbond_it 4.29 r_scbond_other 4.284
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.962 r_dihedral_angle_3_deg 17.975 r_long_range_B_other 8.574 r_long_range_B_refined 8.573 r_dihedral_angle_1_deg 7.377 r_scangle_other 6.547 r_mcangle_it 5.351 r_mcangle_other 5.351 r_scbond_it 4.29 r_scbond_other 4.284 r_mcbond_it 3.595 r_mcbond_other 3.595 r_angle_refined_deg 1.417 r_angle_other_deg 0.531 r_chiral_restr 0.064 r_bond_other_d 0.009 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 10698 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Coot model building SCALA data scaling PHASER phasing