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Crystal structure of MoCVNH3 variant (Mo0v) in complex with (N-GlcNAc)4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L5B 1L5B,1Y7M experimental model PDB 1Y7M 1L5B,1Y7M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 298 ~8-10 % (w/v) PEG 3350, 0.1 M sodium phosphate-citrate buffer, pH 4.2, 0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.23 44.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.72 α = 90 b = 50.277 β = 103.53 c = 43.132 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 100 CCD RIGAKU SATURN 944 2011-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 41.94 98.7 0.098 9 4.03 11980
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 97 0.257 2.2 2.51
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 1L5B,1Y7M 1.9 41.94 10800 1180 98.61 0.22677 0.2235 0.25583 0.2683 RANDOM 32.178
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] -13.77 -4.1 -2.91 16.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.91 r_dihedral_angle_4_deg 15.925 r_dihedral_angle_3_deg 14.68 r_dihedral_angle_1_deg 6.745 r_scangle_it 2.845 r_scbond_it 1.824 r_angle_refined_deg 1.409 r_mcangle_it 1.042 r_mcbond_it 0.605 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.91 r_dihedral_angle_4_deg 15.925 r_dihedral_angle_3_deg 14.68 r_dihedral_angle_1_deg 6.745 r_scangle_it 2.845 r_scbond_it 1.824 r_angle_refined_deg 1.409 r_mcangle_it 1.042 r_mcbond_it 0.605 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1201 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction Coot model building PHASER phasing d*TREK data scaling