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Crystal Structure of Hyperthermophilic Endo-beta-1,4-glucanase in complex with substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RJX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 291 1.2M NaH2PO4/KH2PO4 (1:1), 0.1M sodium citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.02 38.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.3 α = 90 b = 47.3 β = 90 c = 271.387 γ = 90
Symmetry Space Group P 41 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 100 CCD ADSC QUANTUM 315 2009-11-03 M SINGLE WAVELENGTH 2 1 100 CCD MARMOSAIC 225 mm CCD 2009-11-22 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A 2 SYNCHROTRON BSRF BEAMLINE 1W2B 1.0000 BSRF 1W2B 3 SYNCHROTRON SSRF BEAMLINE BL17U 1.0000 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 50 98 16953 16724
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 3RJX 2.2 46.57 15843 845 99.32 0.19039 0.18723 0.1865 0.25276 0.2521 RANDOM 28.968
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] 0.18 0.18 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.348 r_dihedral_angle_4_deg 21.266 r_dihedral_angle_3_deg 13.949 r_dihedral_angle_1_deg 5.921 r_scangle_it 2.414 r_scbond_it 1.571 r_angle_refined_deg 1.298 r_mcangle_it 0.946 r_mcbond_it 0.61 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.348 r_dihedral_angle_4_deg 21.266 r_dihedral_angle_3_deg 13.949 r_dihedral_angle_1_deg 5.921 r_scangle_it 2.414 r_scbond_it 1.571 r_angle_refined_deg 1.298 r_mcangle_it 0.946 r_mcbond_it 0.61 r_nbtor_refined 0.314 r_symmetry_hbond_refined 0.214 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.093 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2594 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 41
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling