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Structure of PipY, the COG0325 family member of Synechococcus elongatus PCC7942,without PLP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W8G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 294 0.1 M Tris-HCl, pH 8.5
0.2 M Magnesium chloride
25% (wt/vol) Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 1.97 37.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.618 α = 90 b = 41.778 β = 108.15 c = 77.761 γ = 90
Symmetry Space Group P 1 21 1
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 2016-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9792 ALBA XALOC
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 1.9 44.61 99.7 0.045 0.023 0.998 20.6 4.6 32801
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 99.2 0.17 0.935 4 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 FREE R-VALUE 1w8g 1.9 44.61 31157 1632 99.56 0.15963 0.15719 0.1673 0.20744 0.2152 RANDOM 27.196
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] 0.11 -0.38 0.59 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.075 r_dihedral_angle_4_deg 17.04 r_dihedral_angle_3_deg 13.137 r_dihedral_angle_1_deg 6.176 r_long_range_B_refined 4.98 r_long_range_B_other 4.819 r_scangle_other 2.73 r_angle_refined_deg 1.835 r_mcangle_other 1.785 r_mcangle_it 1.784
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.075 r_dihedral_angle_4_deg 17.04 r_dihedral_angle_3_deg 13.137 r_dihedral_angle_1_deg 6.176 r_long_range_B_refined 4.98 r_long_range_B_other 4.819 r_scangle_other 2.73 r_angle_refined_deg 1.835 r_mcangle_other 1.785 r_mcangle_it 1.784 r_scbond_it 1.7 r_scbond_other 1.687 r_mcbond_it 1.111 r_mcbond_other 1.105 r_angle_other_deg 1.043 r_chiral_restr 0.107 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 3313 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction