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Crystal structure of Sorbitol-6-Phosphate 2-dehydrogenase SrlD from Erwinia amylovora
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GEG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 277 100 mM HEPES pH 7.5, 600 mM MgCl2, 17% PEG3350 (cryo 20% Ethylene glycol)
Crystal Properties Matthews coefficient Solvent content 2.46 49.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.707 α = 90 b = 138.057 β = 90 c = 199.442 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 100 PIXEL DECTRIS PILATUS 6M 2015-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91730 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.84 113.51 99 9.3 4.5 284126
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 1.95 97.6 2.2 4.4
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 1GEG 1.84 113.51 267165 14179 97.96 0.22384 0.209 0.2211 0.255 0.2672 RANDOM 29.31
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] -0.56 -0.81 1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.647 r_dihedral_angle_4_deg 17.364 r_dihedral_angle_3_deg 14.513 r_dihedral_angle_1_deg 6.947 r_long_range_B_refined 5.096 r_long_range_B_other 5.095 r_scangle_other 3.727 r_mcangle_it 2.934 r_mcangle_other 2.934 r_scbond_it 2.477
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.647 r_dihedral_angle_4_deg 17.364 r_dihedral_angle_3_deg 14.513 r_dihedral_angle_1_deg 6.947 r_long_range_B_refined 5.096 r_long_range_B_other 5.095 r_scangle_other 3.727 r_mcangle_it 2.934 r_mcangle_other 2.934 r_scbond_it 2.477 r_scbond_other 2.477 r_mcbond_it 2.03 r_mcbond_other 2.03 r_angle_refined_deg 1.881 r_angle_other_deg 1.081 r_chiral_restr 0.121 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.002 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 23365 Nucleic Acid Atoms Solvent Atoms 778 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing