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Crystal structure of the GH51 arabinofuranosidase from Xanthomonas axonopodis pv. citri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VRQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 17% (w/v) polyethylene glycol 3350 and 0.2 M ammonium chloride
Crystal Properties Matthews coefficient Solvent content 2.37 48.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.344 α = 90 b = 163.231 β = 107.57 c = 114.425 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 PIXEL DECTRIS PILATUS 6M 2015-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.979500 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.91 48.74 95.1 0.095 0.113 0.996 9.74 3.429 236094 28.412
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.91 2.03 80.3 0.514 0.639 0.729 2.06 2.81
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 2VRQ 1.91 48.74 234093 2000 95.76 0.1488 0.1487 0.1581 0.1667 0.1762 RANDOM 23.528
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] 0.66 0.22 -0.22 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.066 r_dihedral_angle_4_deg 20.203 r_dihedral_angle_3_deg 12.501 r_dihedral_angle_1_deg 6.564 r_angle_refined_deg 1.509 r_angle_other_deg 0.527 r_chiral_restr 0.073 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.066 r_dihedral_angle_4_deg 20.203 r_dihedral_angle_3_deg 12.501 r_dihedral_angle_1_deg 6.564 r_angle_refined_deg 1.509 r_angle_other_deg 0.527 r_chiral_restr 0.073 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23035 Nucleic Acid Atoms Solvent Atoms 2384 Heterogen Atoms 36
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction