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Crystal structure of metagenome-derived glycoside hydrolase family 12 endoglucanase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H0B PDB ENTRY 1H0B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.1M HEPES, 0.2M sodium chloride, 23% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.26 45.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.779 α = 90 b = 59.576 β = 122.89 c = 74.95 γ = 90
Symmetry Space Group C 1 2 1
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 2013-05-26 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 1.85 50 99.4 0.12 21.8 7.2 41281 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 1H0B 1.85 33.36 39135 2075 99 0.16171 0.1596 0.1618 0.20008 0.2052 RANDOM 16.678
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] 1.05 -0.93 -1.13 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.398 r_dihedral_angle_4_deg 19.381 r_dihedral_angle_3_deg 14.557 r_dihedral_angle_1_deg 7.743 r_scangle_it 5.58 r_scbond_it 3.731 r_mcangle_it 2.506 r_mcbond_it 1.566 r_angle_refined_deg 1.2 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.398 r_dihedral_angle_4_deg 19.381 r_dihedral_angle_3_deg 14.557 r_dihedral_angle_1_deg 7.743 r_scangle_it 5.58 r_scbond_it 3.731 r_mcangle_it 2.506 r_mcbond_it 1.566 r_angle_refined_deg 1.2 r_chiral_restr 0.115 r_gen_planes_refined 0.016 r_bond_refined_d 0.012 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 3594 Nucleic Acid Atoms Solvent Atoms 507 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling