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Serine Palmitoyltransferase K265A from S. paucimobilis with bound PLP- Myriocin Aldimine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JG2 PDB ENTRY 2JG2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 32% PEG MME 2000, 0.1M HEPES PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.25 45.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.91 α = 90 b = 98.71 β = 90 c = 133.19 γ = 90
Symmetry Space Group P 21 21 21
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 2M MIRRORS 2012-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 1.62 56.14 98.9 0.07 10.8 3.6 103044 2
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 1.62 1.66 99.7 0.5 2.3 3.8
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 PDB ENTRY 2JG2 1.62 56.14 97821 5148 98.71 0.18998 0.18886 0.1997 0.21086 0.2208 RANDOM 19.736
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] 0.09 -0.76 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.476 r_dihedral_angle_4_deg 14.202 r_dihedral_angle_3_deg 12.542 r_dihedral_angle_1_deg 5.381 r_angle_refined_deg 1.44 r_angle_other_deg 0.983 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.476 r_dihedral_angle_4_deg 14.202 r_dihedral_angle_3_deg 12.542 r_dihedral_angle_1_deg 5.381 r_angle_refined_deg 1.44 r_angle_other_deg 0.983 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.003 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5919 Nucleic Acid Atoms Solvent Atoms 567 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing