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Crystal structure of B30.2 PRYSPRY domain of MID2
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 6.5 293.15 18% High molecular weight PEG smears, 0.1M ADA pH 6.5, 0.2M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.17 43.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.921 α = 90 b = 75.084 β = 90 c = 78.19 γ = 90
Symmetry Space Group C 2 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 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 1.57 48.67 99.9 0.06 0.066 0.02 1 20.8 11.2 26626
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 1.57 1.61 99.8 0.889 0.981 0.287 0.905 2.8 11.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6jbm 1.57 48.67 25278 1327 99.86 0.1639 0.1624 0.163 0.1921 0.1924 RANDOM 24.777
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] -0.06 0.91 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.372 r_dihedral_angle_4_deg 17.837 r_dihedral_angle_3_deg 12.639 r_dihedral_angle_1_deg 7.919 r_angle_refined_deg 1.654 r_angle_other_deg 1.38 r_chiral_restr 0.103 r_gen_planes_refined 0.017 r_bond_refined_d 0.016 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.372 r_dihedral_angle_4_deg 17.837 r_dihedral_angle_3_deg 12.639 r_dihedral_angle_1_deg 7.919 r_angle_refined_deg 1.654 r_angle_other_deg 1.38 r_chiral_restr 0.103 r_gen_planes_refined 0.017 r_bond_refined_d 0.016 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1359 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 41
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing