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The crystal structure of human MACROD2 in space group P41212
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 = 95.65 α = 90 b = 95.65 β = 90 c = 258.72 γ = 90
Symmetry Space Group P 41 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 6M-F 2017-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9762 ESRF ID23-1
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 1.75 47.83 100 0.107 0.112 0.998 13.27 12.116 121564 37.437
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 1.75 1.8 100 1.542 1.613 0.709 1.7 11.75
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 4IQY 1.75 47.83 115484 6079 99.98 0.2055 0.2043 0.2274 0.2403 RANDOM 33.887
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] 1.01 1.01 -2.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.1 r_dihedral_angle_4_deg 17.185 r_dihedral_angle_3_deg 14.309 r_dihedral_angle_1_deg 6.805 r_angle_refined_deg 1.439 r_angle_other_deg 1.343 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.1 r_dihedral_angle_4_deg 17.185 r_dihedral_angle_3_deg 14.309 r_dihedral_angle_1_deg 6.805 r_angle_refined_deg 1.439 r_angle_other_deg 1.343 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6830 Nucleic Acid Atoms Solvent Atoms 511 Heterogen Atoms 10
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction