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Crystal waters on the nine polyproline type II helical bundle springtail antifreeze protein from Granisotoma rainieri match the ice lattice
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PNE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 277.15 0.2 M lithium nitrate, 2.2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 1.95 37.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.489 α = 90 b = 64.214 β = 90 c = 86.267 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 PILATUS3 S 6M 2019-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9795 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.21 43.171 99.9 0.064 0.067 0.019 0.999 16.5 12.4 52608
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.21 1.23 99.7 0.925 0.963 0.266 0.923 2.5 12.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2PNE 1.21 43.171 52554 2636 99.846 0.151 0.1489 0.1539 0.1804 0.1854 18.855
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] 1.659 -1.163 -0.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.844 r_dihedral_angle_3_deg 12.518 r_dihedral_angle_1_deg 6.907 r_rigid_bond_restr 5.746 r_scangle_it 4.304 r_scangle_other 4.304 r_scbond_it 4.223 r_scbond_other 4.207 r_lrange_it 4.023 r_lrange_other 3.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.844 r_dihedral_angle_3_deg 12.518 r_dihedral_angle_1_deg 6.907 r_rigid_bond_restr 5.746 r_scangle_it 4.304 r_scangle_other 4.304 r_scbond_it 4.223 r_scbond_other 4.207 r_lrange_it 4.023 r_lrange_other 3.912 r_mcangle_it 2.963 r_mcangle_other 2.962 r_mcbond_it 2.408 r_mcbond_other 2.396 r_angle_refined_deg 2.115 r_angle_other_deg 2.085 r_nbd_other 0.201 r_symmetry_xyhbond_nbd_refined 0.192 r_symmetry_nbd_other 0.186 r_xyhbond_nbd_refined 0.175 r_symmetry_nbd_refined 0.17 r_nbd_refined 0.166 r_nbtor_refined 0.152 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.076 r_bond_refined_d 0.017 r_bond_other_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1381 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing