☰ Navigation Tabs
The 3-dimensional structure of a thermostable mutant of a xylanase (Xyn10A) from Cellvibrio japonicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CLX PDB ENTRY 1CLX
Crystallization Crystal Properties Matthews coefficient Solvent content 2.2 44.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.609 α = 90 b = 95.609 β = 90 c = 150.315 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 120 2002-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 1.55 25 100 0.08 31.96 9.6 100882
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 1.55 1.61 100 0.29 10.07 11.1
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 1.55 25 95756 5034 100 0.151 0.149 0.1632 0.186 0.1944 RANDOM 14.92
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] -0.02 -0.02 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.986 r_dihedral_angle_4_deg 17.74 r_dihedral_angle_3_deg 12.529 r_dihedral_angle_1_deg 6.618 r_scangle_it 3.268 r_scbond_it 2.415 r_mcangle_it 1.648 r_angle_refined_deg 1.452 r_mcbond_it 1.218 r_angle_other_deg 0.774
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.986 r_dihedral_angle_4_deg 17.74 r_dihedral_angle_3_deg 12.529 r_dihedral_angle_1_deg 6.618 r_scangle_it 3.268 r_scbond_it 2.415 r_mcangle_it 1.648 r_angle_refined_deg 1.452 r_mcbond_it 1.218 r_angle_other_deg 0.774 r_symmetry_vdw_other 0.305 r_xyhbond_nbd_refined 0.285 r_symmetry_hbond_refined 0.252 r_nbd_refined 0.25 r_nbd_other 0.235 r_nbtor_refined 0.193 r_symmetry_vdw_refined 0.13 r_nbtor_other 0.096 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 5412 Nucleic Acid Atoms Solvent Atoms 711 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing