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The crystal structure of human MACROD2 in space group P43212
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IQY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 293 0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.36 α = 90 b = 95.36 β = 90 c = 261.92 γ = 90
Symmetry Space Group P 43 21 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 2M 2019-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9762 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.9 47.73 100 0.081 0.085 1 18.92 13.348 95967 42.232
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 100 1.65 1.729 0.746 1.25 11.395
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 4IQY 1.9 47.73 91202 4765 99.95 0.2018 0.2005 0.2099 0.2277 0.2097 RANDOM 42.981
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] 1.68 1.68 -3.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.444 r_dihedral_angle_4_deg 18.353 r_dihedral_angle_3_deg 16.958 r_dihedral_angle_1_deg 6.744 r_angle_refined_deg 1.563 r_angle_other_deg 1.367 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.444 r_dihedral_angle_4_deg 18.353 r_dihedral_angle_3_deg 16.958 r_dihedral_angle_1_deg 6.744 r_angle_refined_deg 1.563 r_angle_other_deg 1.367 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6856 Nucleic Acid Atoms Solvent Atoms 440 Heterogen Atoms 10
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing