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Structure of glycerol dehydrogenase crystallised as a contaminant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MCA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 295 0.1 M HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid), pH 7.5, 0.02 M magnesium chloride hexahydrate
Crystal Properties Matthews coefficient Solvent content 4.09 69.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.55 α = 90 b = 178.55 β = 90 c = 80.09 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 2014-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54
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 2.33 56.46 89.3 0.2 0.98 8.07 6.8 96487
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 2.33 2.39 51.9 0.37 0.64 1.3
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 4MCA 2.33 56.46 91655 4831 89.31 0.23676 0.23598 0.2376 0.25146 0.2524 RANDOM 33.661
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] 9.29 9.29 -18.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.946 r_dihedral_angle_4_deg 18.69 r_dihedral_angle_3_deg 14.351 r_dihedral_angle_1_deg 5.541 r_long_range_B_refined 2.677 r_long_range_B_other 2.66 r_mcangle_it 1.522 r_mcangle_other 1.522 r_scangle_other 1.395 r_angle_refined_deg 1.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.946 r_dihedral_angle_4_deg 18.69 r_dihedral_angle_3_deg 14.351 r_dihedral_angle_1_deg 5.541 r_long_range_B_refined 2.677 r_long_range_B_other 2.66 r_mcangle_it 1.522 r_mcangle_other 1.522 r_scangle_other 1.395 r_angle_refined_deg 1.198 r_mcbond_it 0.94 r_mcbond_other 0.94 r_angle_other_deg 0.912 r_scbond_it 0.877 r_scbond_other 0.875 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 10932 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement xia2 data processing PHASER phasing