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Structure of the Thermotoga maritima Family 5 endo-glucanase in complex with 1-deoxynojiromycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VJZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100 mM sodium citrate tribasic dihydrate (pH 5.8-6.2), 8-14% (v/v) isopropanol, 8-16% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.37 48.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.33 α = 90 b = 62.28 β = 90 c = 202.69 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 IMAGE PLATE MAR scanner 345 mm plate Mirrors 2014-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.8 42.72 95 0.05 0.054 0.018 0.999 24.7 7.2 69266 14.91
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 71.5 0.181 0.213 0.111 0.964 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1VJZ 1.8 39.306 1.34 69136 2104 94.77 0.1417 0.1409 0.1416 0.1681 0.1689 17.7993
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.528 f_angle_d 0.808 f_chiral_restr 0.052 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5384 Nucleic Acid Atoms Solvent Atoms 898 Heterogen Atoms 72
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing