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Crystal structure of Mitsuba-1 with bound NAcGal
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M MES pH 6.5, 25 % PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.13 42.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.782 α = 90 b = 38.677 β = 97.56 c = 42.761 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 97 PIXEL DECTRIS PILATUS3 S 6M 2015-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.54 50 94.5 0.063 0.075 0.04 17.9 2.9 19585
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 1.55 1.58 85.3 0.215 0.272 0.163 0.901 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.54 42.41 18576 1004 93.78 0.1521 0.1497 0.1619 0.1973 0.2072 RANDOM 14.398
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] -0.71 -0.75 1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.495 r_dihedral_angle_4_deg 22.996 r_dihedral_angle_3_deg 13.769 r_dihedral_angle_1_deg 8.571 r_angle_refined_deg 2.194 r_angle_other_deg 1.005 r_chiral_restr 0.158 r_bond_refined_d 0.022 r_gen_planes_refined 0.014 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.495 r_dihedral_angle_4_deg 22.996 r_dihedral_angle_3_deg 13.769 r_dihedral_angle_1_deg 8.571 r_angle_refined_deg 2.194 r_angle_other_deg 1.005 r_chiral_restr 0.158 r_bond_refined_d 0.022 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1160 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 45
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction MOLREP phasing