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Semi-active E176Q mutant of rice BGlu1, a plant exoglucanase/beta-glucosidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CBG PDB ENTRY 1CBG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 288 20% PEG MME 5000, 0.18M ammonium sulfate, 0.1M MES, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.35 47.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.81 α = 90 b = 101.04 β = 90 c = 127.606 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 105 CCD ADSC QUANTUM 315 2006-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 0.98 NSRRC BL13B1
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 1.65 30 99.7 0.056 17.38 2.7 124354
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 1.65 1.71 99.6 0.325 3.12 2.6 23896
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 1CBG 1.65 28.12 118005 6166 99.71 0.17503 0.17391 0.1731 0.19647 0.1952 Copy R-free from 2RGL 13.382
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 r_dihedral_angle_2_deg 34.922 r_dihedral_angle_4_deg 22.306 r_dihedral_angle_3_deg 12.181 r_dihedral_angle_1_deg 5.942 r_scangle_it 2.985 r_scbond_it 1.957 r_angle_refined_deg 1.357 r_mcangle_it 1.096 r_mcbond_it 0.695 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.922 r_dihedral_angle_4_deg 22.306 r_dihedral_angle_3_deg 12.181 r_dihedral_angle_1_deg 5.942 r_scangle_it 2.985 r_scbond_it 1.957 r_angle_refined_deg 1.357 r_mcangle_it 1.096 r_mcbond_it 0.695 r_nbtor_refined 0.315 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.193 r_symmetry_hbond_refined 0.166 r_chiral_restr 0.162 r_xyhbond_nbd_refined 0.12 r_metal_ion_refined 0.025 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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_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 7618 Nucleic Acid Atoms Solvent Atoms 895 Heterogen Atoms 59
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling