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Crystal Structure of apo-mannanase 26A from Psudomonas cellulosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J9Y PDB ENTRY 1J9Y
Crystallization Crystal Properties Matthews coefficient Solvent content 2.46 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.24 α = 90 b = 93.24 β = 90 c = 54.83 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate TRIANGULAR MONOCHROMATOR AND BENT MIRROR 1999-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
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 91.29 99.8 0.033 29.9 40381 40381 -1 -1
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) 1.85 1.898 99.4 0.077 10.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT PDB ENTRY 1J9Y 1.85 91.29 38213 38213 2021 99.48 0.14611 0.14611 0.14489 0.1592 0.17004 RANDOM 14.753
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] -0.49 -0.49 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.649 r_scangle_it 2.515 r_scbond_it 1.48 r_angle_refined_deg 1.346 r_mcangle_it 1.04 r_angle_other_deg 0.803 r_mcbond_it 0.562 r_symmetry_vdw_other 0.254 r_nbd_other 0.242 r_nbd_refined 0.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.649 r_scangle_it 2.515 r_scbond_it 1.48 r_angle_refined_deg 1.346 r_mcangle_it 1.04 r_angle_other_deg 0.803 r_mcbond_it 0.562 r_symmetry_vdw_other 0.254 r_nbd_other 0.242 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.166 r_metal_ion_refined 0.164 r_xyhbond_nbd_refined 0.163 r_symmetry_hbond_refined 0.124 r_nbtor_other 0.081 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2916 Nucleic Acid Atoms Solvent Atoms 521 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling