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Structure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with nickel
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5M17
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 292 100 mM MIB buffer, pH 6.0.
Protein at 5.5 mg/ml in 50 mM potassium phosphate, 50 mM KCl.
150 nl protein solution and 150 nl reservoir solution.
Crystal Properties Matthews coefficient Solvent content 2.53 51.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.467 α = 90 b = 86.535 β = 90 c = 135.916 γ = 90
Symmetry Space Group P 2 21 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 PILATUS 6M 2017-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 2.25 135.92 98.1 0.2 0.21 0.061 0.994 7 11.4 21876 40.95
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 2.25 2.33 84.5 1.872 2.029 0.75 0.345 0.9 6.9
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 (All) 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 5M17 2.251 73.103 21817 1106 97.764 0.179 0.1769 0.1881 0.2234 0.23 RANDOM 47.23
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] -0.734 -2.644 3.378
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.041 r_dihedral_angle_3_deg 15.072 r_dihedral_angle_4_deg 14.786 r_lrange_it 8.161 r_lrange_other 8.116 r_dihedral_angle_1_deg 6.494 r_scangle_it 5.529 r_scangle_other 5.527 r_mcangle_it 5.338 r_mcangle_other 5.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.041 r_dihedral_angle_3_deg 15.072 r_dihedral_angle_4_deg 14.786 r_lrange_it 8.161 r_lrange_other 8.116 r_dihedral_angle_1_deg 6.494 r_scangle_it 5.529 r_scangle_other 5.527 r_mcangle_it 5.338 r_mcangle_other 5.337 r_scbond_it 3.47 r_scbond_other 3.469 r_mcbond_it 3.412 r_mcbond_other 3.408 r_angle_other_deg 2.341 r_angle_refined_deg 1.889 r_nbd_other 0.246 r_symmetry_nbd_refined 0.208 r_nbd_refined 0.202 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.182 r_symmetry_xyhbond_nbd_refined 0.176 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.134 r_symmetry_xyhbond_nbd_other 0.112 r_symmetry_nbtor_other 0.079 r_bond_other_d 0.035 r_bond_refined_d 0.015 r_gen_planes_other 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2877 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing