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Crystal structure of beta-1,3-glucanase from Phanerochaete chrysosporium (Lam55A) gluconolactone complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EQN PDB ENTRY 3EQN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 298 15% PEG 3350, 0.1M zinc acetate, 0.05M MES-NaOH, 10% glycerol, 2% ethanol, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.89 57.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.534 α = 93.94 b = 67.146 β = 106.76 c = 109.778 γ = 97.08
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 2006-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.25 50 91.9 0.097 10.9 3.4 84385 77511 24.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.33 74.5 0.257 2.7 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3EQN 2.25 31.5 77511 73632 3875 91.48 0.14473 0.14178 0.1439 0.20019 0.2025 RANDOM 21.031
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.45 r_dihedral_angle_4_deg 14.615 r_dihedral_angle_3_deg 14.429 r_dihedral_angle_1_deg 8.007 r_scangle_it 3.571 r_scbond_it 2.399 r_angle_refined_deg 1.805 r_mcangle_it 1.429 r_mcbond_it 0.862 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.45 r_dihedral_angle_4_deg 14.615 r_dihedral_angle_3_deg 14.429 r_dihedral_angle_1_deg 8.007 r_scangle_it 3.571 r_scbond_it 2.399 r_angle_refined_deg 1.805 r_mcangle_it 1.429 r_mcbond_it 0.862 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.222 r_nbd_refined 0.204 r_symmetry_hbond_refined 0.175 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.125 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 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 11222 Nucleic Acid Atoms Solvent Atoms 1193 Heterogen Atoms 104
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling