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Crystal structure of the Gracilariopsis lemaneiformis alpha- 1,4-glucan lyase with deoxynojirimycin
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, 0.1 M 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 = 134.314 α = 90 b = 91.707 β = 99.33 c = 192.899 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 110 IMAGE PLATE MAC Science DIP-2030 OSMIC MIRRORS 2007-03-01 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 2.35 50 91 0.21 4.3 4 175340 -3 33.5
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 2.35 2.43 85.2 0.69 1 2
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 2.35 33.19 166607 8712 90.98 0.23673 0.23387 0.2356 0.29121 0.2965 RANDOM 46.07
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] 2.57 -2.95 -1.99 -1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.389 r_dihedral_angle_4_deg 17.333 r_dihedral_angle_3_deg 16.103 r_dihedral_angle_1_deg 8.938 r_angle_refined_deg 1.301 r_scangle_it 0.148 r_scbond_it 0.117 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.389 r_dihedral_angle_4_deg 17.333 r_dihedral_angle_3_deg 16.103 r_dihedral_angle_1_deg 8.938 r_angle_refined_deg 1.301 r_scangle_it 0.148 r_scbond_it 0.117 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_mcangle_it 0.004 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_it 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 1577 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing