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Crystal structure of endo-xylogalacturonan hydrolase from Aspergillus tubingensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NHC PDB ENTRIES 1NHC, 1RMG, 1CZF AND 2IQ7 experimental model PDB 1RMG PDB ENTRIES 1NHC, 1RMG, 1CZF AND 2IQ7 experimental model PDB 1CZF PDB ENTRIES 1NHC, 1RMG, 1CZF AND 2IQ7 experimental model PDB 2IQ7 PDB ENTRIES 1NHC, 1RMG, 1CZF AND 2IQ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.4 298 2.9 M AMMONIUM SULFATE, 0.1 M NA-ACETATE BUFFER PH 4.4, VAPOR DIFFUSION, HANGING DROP, 298 K
Crystal Properties Matthews coefficient Solvent content 3.8 67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.44 α = 90 b = 121.18 β = 90 c = 129.67 γ = 90
Symmetry Space Group I 2 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 ADSC QUANTUM 315r 2010-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.75 40.7 99.8 0.1 11.6 7.1 60896 -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 1.75 1.84 100 0.58 3.7 7.2
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 ENTRIES 1NHC, 1RMG, 1CZF AND 2IQ7 1.75 88.54 57809 3084 99.9 0.16846 0.16734 0.1678 0.18927 0.1896 RANDOM 20.587
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] 0.41 -0.47 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.957 r_dihedral_angle_4_deg 19.223 r_dihedral_angle_3_deg 10.835 r_dihedral_angle_1_deg 5.734 r_angle_refined_deg 1.327 r_chiral_restr 0.087 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.957 r_dihedral_angle_4_deg 19.223 r_dihedral_angle_3_deg 10.835 r_dihedral_angle_1_deg 5.734 r_angle_refined_deg 1.327 r_chiral_restr 0.087 r_bond_refined_d 0.008 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 2690 Nucleic Acid Atoms Solvent Atoms 458 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing