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Crystal structure of non-toxic HaNLP3 protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GNZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M di-ammonium hydrogen phosphate, 20 % (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.54 51.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.673 α = 90 b = 48.879 β = 90 c = 112.333 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 a vertical collimating mirror, a double-crystal Si(111) monochromator, a bendable focussing mirror 2014-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2 41.511 94 0.172 0.189 0.979 8.51 6.157 16264 19.24
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.12 99.3 0.303 0.33 0.942 5.39 6.436
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3GNZ 2 41.511 1.38 16262 1626 94.13 0.1846 0.1817 0.1822 0.2112 0.2107 23.8123
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.726 f_angle_d 1.116 f_chiral_restr 0.059 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1687 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 102
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction