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Crystal structure of the Gracilariopsis lemaneiformis alpha-1,4- glucan lyase with acarbose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X2H PDB ENTRY 2X2H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 18-21% PEG 8000, 0.1M SODIUM ACETATE, PH 5.0-5.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.861 α = 90 b = 91.804 β = 99.34 c = 193.349 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 112 IMAGE PLATE MACSCIENCE DIP2030H FRANKS MIRRORS 2006-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.6 50 82.8 0.23 4.6 2.7 118187 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 79.3 0.64 1 2.1
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 PDB ENTRY 2X2H 2.6 41.85 112226 5895 82.2 0.23385 0.2293 0.233 0.3204 0.3226 RANDOM 40.005
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] 2.22 -2.39 -2.51 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.036 r_dihedral_angle_4_deg 17.343 r_dihedral_angle_3_deg 17.334 r_dihedral_angle_1_deg 8.592 r_angle_refined_deg 1.275 r_mcangle_it 1.096 r_scangle_it 0.816 r_mcbond_it 0.636 r_scbond_it 0.534 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.036 r_dihedral_angle_4_deg 17.343 r_dihedral_angle_3_deg 17.334 r_dihedral_angle_1_deg 8.592 r_angle_refined_deg 1.275 r_mcangle_it 1.096 r_scangle_it 0.816 r_mcbond_it 0.636 r_scbond_it 0.534 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32648 Nucleic Acid Atoms Solvent Atoms 836 Heterogen Atoms 350
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing