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UDP-GlcNAc 2-epimerase MnaA of Paenibacillus alvei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other Phyre2-predicted model of Paenibacillus alvei MnaA
Crystallization Crystalization Experiments ID Method pH Temperature Details 2 VAPOR DIFFUSION, HANGING DROP 8.8 291.15 0.16 M CaCl2, 0.1 M Tris/HCl pH 8.8, and 15% PEG 4000
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.816 α = 90 b = 81.763 β = 97.14 c = 107.722 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 PIXEL DECTRIS PILATUS 200K 2020-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.2 50 99 0.057 0.065 0.031 0.998 17.5 4 39705
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 2.2 2.28 91.4 0.211 0.251 0.133 0.957 3
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 MOLECULAR REPLACEMENT THROUGHOUT 2.2 50 37651 2017 99.17 0.2125 0.20979 0.2148 0.26327 0.2649 RANDOM 32.542
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] -1.97 -1.29 3.83 -1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.669 r_dihedral_angle_4_deg 21.034 r_dihedral_angle_3_deg 19.305 r_dihedral_angle_1_deg 7.404 r_long_range_B_refined 7.065 r_long_range_B_other 7.06 r_scangle_other 4.962 r_mcangle_it 4.335 r_mcangle_other 4.335 r_scbond_it 3.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.669 r_dihedral_angle_4_deg 21.034 r_dihedral_angle_3_deg 19.305 r_dihedral_angle_1_deg 7.404 r_long_range_B_refined 7.065 r_long_range_B_other 7.06 r_scangle_other 4.962 r_mcangle_it 4.335 r_mcangle_other 4.335 r_scbond_it 3.141 r_scbond_other 3.14 r_mcbond_it 2.85 r_mcbond_other 2.846 r_angle_refined_deg 1.662 r_angle_other_deg 1.301 r_chiral_restr 0.085 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5646 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing