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Structure of modular Xyn30D from Paenibacillus barcinonensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GTN pdb entry 3GTN, 2VZP experimental model PDB 2VZP pdb entry 3GTN, 2VZP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 10% PEG 3350, 5% Glycerol, 0.1M Tris, Streak Seeding (2:1), pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.06 59.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.06 α = 90 b = 174.06 β = 90 c = 183.932 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 PIXEL DECTRIS PILATUS 2M-F 2011-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.4 40.77 100 0.143 0.044 14.7 11.4 243818 243713 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 100 0.577 0.178 2.6 11.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3GTN, 2VZP 2.4 40.77 243713 231561 12151 99.98 0.19417 0.19373 0.1896 0.20246 0.1983 RANDOM 12.621
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] -0.26 -0.26 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.972 r_dihedral_angle_4_deg 23.512 r_dihedral_angle_3_deg 14.498 r_dihedral_angle_1_deg 6.903 r_long_range_B_refined 2.503 r_long_range_B_other 2.502 r_mcangle_other 1.542 r_mcangle_it 1.192 r_angle_refined_deg 1.18 r_scangle_other 1.176
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.972 r_dihedral_angle_4_deg 23.512 r_dihedral_angle_3_deg 14.498 r_dihedral_angle_1_deg 6.903 r_long_range_B_refined 2.503 r_long_range_B_other 2.502 r_mcangle_other 1.542 r_mcangle_it 1.192 r_angle_refined_deg 1.18 r_scangle_other 1.176 r_angle_other_deg 0.762 r_scbond_other 0.679 r_mcbond_it 0.648 r_mcbond_other 0.648 r_scbond_it 0.402 r_chiral_restr 0.072 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 33155 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 16
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling