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Crystal structure of B30.2 PRYSPRY domain of MID1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JBM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.25 293.15 1.1M sodium citrate, 0.1M HEPES 7.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.863 α = 103.76 b = 51.763 β = 92.64 c = 80.38 γ = 94.33
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 EIGER2 X 16M 2020-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00000 SLS X06SA
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 2.07 47.71 95 0.114 0.146 0.07 0.99 5.5 4 35045
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 2.07 2.14 94.6 0.472 0.625 0.303 0.867 2 4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6jbm 2.07 47.71 33313 1721 94.99 0.2291 0.227 0.2726 0.3023 RANDOM 49.382
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] -3.59 -0.48 1.24 2.1 4.62 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.364 r_dihedral_angle_4_deg 16.876 r_dihedral_angle_3_deg 15.299 r_dihedral_angle_1_deg 9.733 r_angle_refined_deg 1.293 r_angle_other_deg 1.143 r_chiral_restr 0.054 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.364 r_dihedral_angle_4_deg 16.876 r_dihedral_angle_3_deg 15.299 r_dihedral_angle_1_deg 9.733 r_angle_refined_deg 1.293 r_angle_other_deg 1.143 r_chiral_restr 0.054 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5259 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing