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Crystal structure of alpha-L-arabinofuranosidase from Thermotoga maritima ligand free form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PZ3 PDB ENTRY 1PZ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 1M sodium citrate, 0.1M Tris-HCl, 0.2M NaCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 3.69 66.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.515 α = 90 b = 160.647 β = 91.75 c = 155.735 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 100 CCD ADSC QUANTUM 210r 2010-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 97.4 0.061 34.1 7.3 458377 446597 22.6
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 1.86 95.6 0.495 3.4 6.6 43730
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 (All) 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 1PZ3 1.8 30.14 446597 422884 22344 97.03 0.17617 0.17617 0.17507 0.1753 0.19686 0.1975 RANDOM 25.144
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.585 r_dihedral_angle_4_deg 17.213 r_dihedral_angle_3_deg 12.094 r_dihedral_angle_1_deg 6.263 r_scangle_it 3.657 r_scbond_it 2.137 r_angle_refined_deg 1.301 r_mcangle_it 1.291 r_mcbond_it 0.695 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.585 r_dihedral_angle_4_deg 17.213 r_dihedral_angle_3_deg 12.094 r_dihedral_angle_1_deg 6.263 r_scangle_it 3.657 r_scbond_it 2.137 r_angle_refined_deg 1.301 r_mcangle_it 1.291 r_mcbond_it 0.695 r_chiral_restr 0.094 r_bond_refined_d 0.013 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 23257 Nucleic Acid Atoms Solvent Atoms 2424 Heterogen Atoms 253
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling