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Structure of PipY, the COG0325 family member of Synechococcus elongatus PCC7942, with PLP bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NLC PDB file 5NLC, chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 0.1 M Hepes-Na pH 7.5
0.2 M Calcium acetate
18% (wt/vol) Polyethylene glycol 8000
Crystal Properties Matthews coefficient Solvent content 2.46 50.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.627 α = 90 b = 98.937 β = 90 c = 103.737 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 PSI PILATUS 6M 2016-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 71.6 99.9 0.067 0.02 0.99 22.3 12.6 37132
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 1.97 98.7 0.051 0.016 0.87 4.5 10.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB file 5NLC, chain A 1.93 71.6 35318 1754 99.84 0.19694 0.19485 0.23821 0.2619 RANDOM 45.399
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] 0.72 -0.63 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.89 r_dihedral_angle_4_deg 17.29 r_dihedral_angle_3_deg 13.54 r_dihedral_angle_1_deg 6.061 r_long_range_B_refined 5.395 r_long_range_B_other 5.364 r_scangle_other 3.342 r_mcangle_it 2.544 r_mcangle_other 2.544 r_scbond_it 2.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.89 r_dihedral_angle_4_deg 17.29 r_dihedral_angle_3_deg 13.54 r_dihedral_angle_1_deg 6.061 r_long_range_B_refined 5.395 r_long_range_B_other 5.364 r_scangle_other 3.342 r_mcangle_it 2.544 r_mcangle_other 2.544 r_scbond_it 2.155 r_scbond_other 2.154 r_angle_refined_deg 1.666 r_mcbond_it 1.646 r_mcbond_other 1.642 r_angle_other_deg 0.994 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 3204 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing BUCCANEER model building