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MlghC, GDP-mannoheptose C4 reductase from Campylobacter jejuni with NADP bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BSV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 24.63 % (w/v) PEG 8000, 0.1 M Bicine pH 8.5, 0.12 M sodium citrate 0.05 % (w/v).
Crystal Properties Matthews coefficient Solvent content 2.75 55.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.8 α = 90 b = 131.96 β = 105.84 c = 59.33 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 PILATUS3 6M 2016-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9282 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 1.66 66 99.2 0.059 1 11.8 3.7 94907
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 1.66 1.7 99 0.76 0.5 3.1
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 1BSV 1.66 65.98 94907 4889 99.17 0.17416 0.17273 0.1854 0.20231 0.2128 RANDOM 26.453
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.985 r_dihedral_angle_4_deg 15.898 r_dihedral_angle_3_deg 12.75 r_long_range_B_refined 8.58 r_long_range_B_other 8.554 r_scangle_other 7.386 r_dihedral_angle_1_deg 5.803 r_scbond_other 5.169 r_scbond_it 5.167 r_mcangle_it 4.438
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.985 r_dihedral_angle_4_deg 15.898 r_dihedral_angle_3_deg 12.75 r_long_range_B_refined 8.58 r_long_range_B_other 8.554 r_scangle_other 7.386 r_dihedral_angle_1_deg 5.803 r_scbond_other 5.169 r_scbond_it 5.167 r_mcangle_it 4.438 r_mcangle_other 4.437 r_mcbond_it 3.359 r_mcbond_other 3.359 r_angle_refined_deg 1.49 r_angle_other_deg 1.205 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5187 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction xia2 data scaling PHASER phasing