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PylD in complex with pyrroline-carboxy-lysine and NADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SeMet-model; coordinates have not been deposited
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M TRIS; 27% PEG3350; 0.2 M Li2SO4, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.44 49.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.25 α = 90 b = 260.98 β = 90 c = 48.6 γ = 90
Symmetry Space Group P 21 21 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 PSI PILATUS 6M 2012-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 1.8 30 92.7 0.059 13.6 3.8 104142 96540 2 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 1.8 1.9 96.6 0.486 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SeMet-model; coordinates have not been deposited 1.8 10 91179 91179 4797 92.2 0.186 0.18061 0.17867 0.1779 0.21766 0.2178 RANDOM 34.313
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] -0.83 0.9 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.734 r_sphericity_free 26.168 r_dihedral_angle_3_deg 14.657 r_sphericity_bonded 12.516 r_dihedral_angle_4_deg 9.673 r_dihedral_angle_1_deg 4.952 r_angle_refined_deg 1.147 r_rigid_bond_restr 0.817 r_chiral_restr 0.068 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.734 r_sphericity_free 26.168 r_dihedral_angle_3_deg 14.657 r_sphericity_bonded 12.516 r_dihedral_angle_4_deg 9.673 r_dihedral_angle_1_deg 4.952 r_angle_refined_deg 1.147 r_rigid_bond_restr 0.817 r_chiral_restr 0.068 r_bond_refined_d 0.005 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7808 Nucleic Acid Atoms Solvent Atoms 558 Heterogen Atoms 252
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling