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Native xylanase10C from Cellvibrio japonicus
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, pH 7.00
Crystal Properties Matthews coefficient Solvent content 2.4 48.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.175 α = 90 b = 78.789 β = 90 c = 172.244 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 TOROIDAL MIRROR 2000-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 99 0.088 16.4 5 52228
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 0.31 5.6 5.3
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 20 49184 2636 99.1 0.162 0.16 0.1607 0.195 0.1948 RANDOM 17.23
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 -0.37 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.21 r_scangle_it 2.941 r_scbond_it 1.977 r_angle_refined_deg 1.392 r_mcangle_it 1.134 r_mcbond_it 0.666 r_symmetry_vdw_refined 0.225 r_nbd_refined 0.194 r_symmetry_hbond_refined 0.139 r_xyhbond_nbd_refined 0.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.21 r_scangle_it 2.941 r_scbond_it 1.977 r_angle_refined_deg 1.392 r_mcangle_it 1.134 r_mcbond_it 0.666 r_symmetry_vdw_refined 0.225 r_nbd_refined 0.194 r_symmetry_hbond_refined 0.139 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.108 r_metal_ion_refined 0.056 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 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_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 3703 Nucleic Acid Atoms Solvent Atoms 681 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing