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Crystal structure of metagenome-derived glycoside hydrolase family 9 endoglucanase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CLC PDB ENTRY 1CLC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1M Tris-HCl, 0.2M Magnesium chloride hexahydrate, 30% w/v Polyethylene glycol 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.35 47.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.631 α = 90 b = 89.913 β = 90 c = 151.157 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 RAYONIX MX225HE 2013-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 2.15 50 99.9 0.133 28 14.9 63355 5
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 1CLC 2.15 43.96 60076 3208 99.72 0.18978 0.18693 0.1881 0.24558 0.2453 RANDOM 43.635
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] -0.71 -0.85 1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.922 r_dihedral_angle_4_deg 21.506 r_dihedral_angle_3_deg 18.051 r_dihedral_angle_1_deg 8.362 r_scangle_it 5.614 r_scbond_it 3.85 r_mcangle_it 2.325 r_mcbond_it 1.446 r_angle_refined_deg 1.19 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.922 r_dihedral_angle_4_deg 21.506 r_dihedral_angle_3_deg 18.051 r_dihedral_angle_1_deg 8.362 r_scangle_it 5.614 r_scbond_it 3.85 r_mcangle_it 2.325 r_mcbond_it 1.446 r_angle_refined_deg 1.19 r_chiral_restr 0.104 r_gen_planes_refined 0.016 r_bond_refined_d 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 8478 Nucleic Acid Atoms Solvent Atoms 397 Heterogen Atoms 6
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling