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The crystal structure of mannitol-1-phosphate dehydrogenase from Shigella flexneri
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 0.1M Na Acetate, pH 5.5, 1.4M Nacitrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.16 61.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.092 α = 90 b = 151.092 β = 90 c = 92.179 γ = 90
Symmetry Space Group I 4 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD SBC-2 mirrors 2009-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9796 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.8 50 100 0.085 52.9 17.8 49634 47419 25.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 100 0.874 3.3 14.8 2450
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.9 50 39865 39865 2125 99.72 0.17588 0.17436 0.204 0.2071 RANDOM 20.141
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] 0.7 0.7 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.202 r_dihedral_angle_4_deg 17.621 r_dihedral_angle_3_deg 13.878 r_dihedral_angle_1_deg 5.411 r_scangle_it 4.247 r_scbond_it 2.7 r_mcangle_it 1.494 r_angle_refined_deg 1.457 r_mcbond_it 0.823 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.202 r_dihedral_angle_4_deg 17.621 r_dihedral_angle_3_deg 13.878 r_dihedral_angle_1_deg 5.411 r_scangle_it 4.247 r_scbond_it 2.7 r_mcangle_it 1.494 r_angle_refined_deg 1.457 r_mcbond_it 0.823 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2862 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 47
Software Software Software Name Purpose HKL-3000 data collection MLPHARE phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling