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Xylanase10C (mutant E385A) from Cellvibrio japonicus in complex with xylopentaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CLX PDB ENTRY 1CLX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 30 MG/ML PROTEIN 0.2 M SODIUM IODIDE, 20% PEG 3350, 20 MM (1 UL) XYLOPENTAOSE, pH 7.00
Crystal Properties Matthews coefficient Solvent content 2.4 48.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.597 α = 90 b = 82.686 β = 90 c = 170.727 γ = 90
Symmetry Space Group P 21 21 21
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 4 VERTICALLY FOCUSSING RH COATED SI MIRROR 2001-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 SRS PX9.6
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 1.85 20 98 0.08 18.5 4.4 53227
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 1.85 1.92 98 0.37 4.8 4.7
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 ENTRY 1CLX 1.85 84.52 50495 2682 97.6 0.181 0.179 0.1824 0.226 0.229 RANDOM 14.72
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] -0.81 -0.52 1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.285 r_scangle_it 2.595 r_scbond_it 1.697 r_angle_refined_deg 1.354 r_mcangle_it 1.007 r_mcbond_it 0.597 r_nbd_refined 0.183 r_symmetry_vdw_refined 0.172 r_xyhbond_nbd_refined 0.142 r_symmetry_hbond_refined 0.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.285 r_scangle_it 2.595 r_scbond_it 1.697 r_angle_refined_deg 1.354 r_mcangle_it 1.007 r_mcbond_it 0.597 r_nbd_refined 0.183 r_symmetry_vdw_refined 0.172 r_xyhbond_nbd_refined 0.142 r_symmetry_hbond_refined 0.141 r_chiral_restr 0.101 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 3910 Nucleic Acid Atoms Solvent Atoms 833 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing