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MlghB, GDP-mannoheptose C3,5 epimerase from Campylobacter jejuni
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DZR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 31.05 % (w/v) PEG 1500, 0.25 M sodium-potassium phosphate, 3.83 % (v/v) 1,4-dioxane)
Crystal Properties Matthews coefficient Solvent content 2.48 50.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.258 α = 90 b = 121.67 β = 90 c = 153.797 γ = 90
Symmetry Space Group P 21 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 120 PIXEL DECTRIS PILATUS3 S 6M 2016-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9159 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.14 95.1 100 0.06 1 12.7 5.9 41762
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.14 2.2 0.76 0.5 1.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1DZR 2.14 77.02 41762 2202 98.13 0.21594 0.21469 0.2248 0.23896 0.247 RANDOM 63.399
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] -0.02 -0.97 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.104 r_dihedral_angle_4_deg 19.733 r_dihedral_angle_3_deg 14.236 r_dihedral_angle_1_deg 7.065 r_long_range_B_refined 6.427 r_long_range_B_other 6.426 r_scangle_other 4.508 r_mcangle_it 3.496 r_mcangle_other 3.496 r_scbond_it 2.983
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.104 r_dihedral_angle_4_deg 19.733 r_dihedral_angle_3_deg 14.236 r_dihedral_angle_1_deg 7.065 r_long_range_B_refined 6.427 r_long_range_B_other 6.426 r_scangle_other 4.508 r_mcangle_it 3.496 r_mcangle_other 3.496 r_scbond_it 2.983 r_scbond_other 2.982 r_mcbond_it 2.366 r_mcbond_other 2.363 r_angle_refined_deg 1.424 r_angle_other_deg 1.002 r_chiral_restr 0.098 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 5637 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing