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Crystal structure of MINDY1 mutant-P138A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JKN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293.15 0.7 M sodium citrate tribasic dihydrate, 0.1 M BIS-TRIS propane pH 7.0
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.649 α = 90 b = 98.649 β = 90 c = 166.073 γ = 90
Symmetry Space Group P 41 2 2
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 6M-F 2018-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97625 ESRF ID23-1
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 3.59 48.28 99.9 0.094 0.1 0.034 0.999 12.5 8.5 10152
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 3.59 3.93 99.9 1.037 1.101 0.368 0.905 8.8
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 5JKN 3.59 48 9595 525 99.78 0.2139 0.2117 0.2581 0.2555 RANDOM 169.231
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] 8.73 8.73 -17.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.513 r_dihedral_angle_3_deg 23.252 r_dihedral_angle_4_deg 18.753 r_dihedral_angle_1_deg 10.126 r_angle_refined_deg 1.67 r_angle_other_deg 1.2 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.513 r_dihedral_angle_3_deg 23.252 r_dihedral_angle_4_deg 18.753 r_dihedral_angle_1_deg 10.126 r_angle_refined_deg 1.67 r_angle_other_deg 1.2 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1946 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction MoRDa phasing