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Crystal structure of Rhagium Mordax antifreeze protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DT5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 295 PEG monomethyl ether 5000, sodium acetate,
magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.67 53.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.457 α = 90 b = 91.143 β = 90 c = 117.447 γ = 90
Symmetry Space Group P 21 2 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 2018-03-14 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) 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 2.05 50 99.7 0.068 0.998 9 13.3 45419
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 2.05 2.11 99.4 0.519 0.835 2 13.7
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 4DT5 2.05 49.413 45380 2230 99.666 0.215 0.2131 0.2177 0.2509 0.2533 32.012
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] -3.624 1.162 2.463
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.032 r_dihedral_angle_4_deg 23.754 r_dihedral_angle_3_deg 11.898 r_lrange_other 9.66 r_lrange_it 9.633 r_dihedral_angle_1_deg 6.32 r_angle_other_deg 1.516 r_angle_refined_deg 1.471 r_mcangle_it 1.071 r_mcangle_other 1.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.032 r_dihedral_angle_4_deg 23.754 r_dihedral_angle_3_deg 11.898 r_lrange_other 9.66 r_lrange_it 9.633 r_dihedral_angle_1_deg 6.32 r_angle_other_deg 1.516 r_angle_refined_deg 1.471 r_mcangle_it 1.071 r_mcangle_other 1.071 r_scangle_it 0.677 r_scangle_other 0.677 r_mcbond_it 0.581 r_mcbond_other 0.581 r_scbond_other 0.417 r_scbond_it 0.412 r_symmetry_nbd_refined 0.272 r_nbd_other 0.25 r_symmetry_nbd_other 0.214 r_nbd_refined 0.173 r_xyhbond_nbd_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.147 r_nbtor_refined 0.127 r_ncsr_local_group_5 0.103 r_ncsr_local_group_2 0.099 r_ncsr_local_group_3 0.097 r_ncsr_local_group_1 0.096 r_ncsr_local_group_9 0.096 r_ncsr_local_group_4 0.093 r_ncsr_local_group_7 0.09 r_ncsr_local_group_6 0.086 r_ncsr_local_group_8 0.084 r_symmetry_nbtor_other 0.082 r_ncsr_local_group_10 0.074 r_chiral_restr 0.054 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4393 Nucleic Acid Atoms Solvent Atoms 514 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing