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Crystal structure of family 11 xylanase in complex with inhibitor (XIP-I)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UKR PDB ENTRY 1UKR, PDB ENTRY 1OMO experimental model PDB 1OMO PDB ENTRY 1UKR, PDB ENTRY 1OMO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 PEG 4000, ammonium sulfate, 1,2,3-heptanetriol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.7 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.748 α = 90 b = 98.748 β = 90 c = 112.095 γ = 90
Symmetry Space Group P 43 21 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 MARRESEARCH 2004-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.97850 SLS X06SA
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 2.5 30 99.8 0.075 0.068 8.5 5.6 19734 60.5
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 2.5 2.64 99.8 0.427 0.387 1.9 5.7 2834
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 (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 1UKR, PDB ENTRY 1OMO 2.5 20 18253 1428 99.74 0.21 0.21288 0.20844 0.2143 0.27091 0.2742 RANDOM 26.836
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] -1.45 -1.45 2.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.52 r_scangle_it 1.99 r_angle_refined_deg 1.127 r_scbond_it 1.097 r_angle_other_deg 1.005 r_mcangle_it 0.7 r_mcbond_it 0.367 r_symmetry_hbond_refined 0.285 r_nbd_other 0.217 r_symmetry_vdw_refined 0.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.52 r_scangle_it 1.99 r_angle_refined_deg 1.127 r_scbond_it 1.097 r_angle_other_deg 1.005 r_mcangle_it 0.7 r_mcbond_it 0.367 r_symmetry_hbond_refined 0.285 r_nbd_other 0.217 r_symmetry_vdw_refined 0.182 r_nbd_refined 0.179 r_xyhbond_nbd_refined 0.174 r_symmetry_vdw_other 0.16 r_nbtor_other 0.086 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3603 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing