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Glc(beta-1-3)Glc disaccharide in -1 and -2 sites of Laminarinase 16A from Phanerochaete chrysosporium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CL2 PDB ENTRY 2CL2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 10 MG/ML LAMINARINASE 16A IN 25 % PEG 3350, 0.2 M AMMONIUM NITRATE AND 10 MM NAOAC PH 5, CO-CRYSTALIZED WITH 10 MM 4-O-BETA-D-GLUCOSYL-LAMINARIBIOSE (G4G3G) LIGAND FOR 6 MONTHS
Crystal Properties Matthews coefficient Solvent content 2.1 40.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.147 α = 90 b = 46.713 β = 90 c = 152.55 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 ADSC CCD DIAMOND (111), GE(220) SAGITALLY FOCUSING GE(220) AND A MULTILAYER 2005-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.1 29.55 88.3 0.06 15.43 3.84 98347 1.9 7
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 1.1 1.11 50.2 0.36 2.3 2.83
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 2CL2 1.1 29.55 1.1 93358 4912 88 0.138 0.138 0.1364 0.152 0.1521 RANDOM 12.38
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] -0.054 0.079 -0.025
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.556 r_dihedral_angle_4_deg 16.647 r_dihedral_angle_3_deg 10.423 r_dihedral_angle_1_deg 7.139 r_scangle_it 2.703 r_scbond_it 1.955 r_mcangle_it 1.551 r_angle_refined_deg 1.45 r_mcbond_it 0.989 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.556 r_dihedral_angle_4_deg 16.647 r_dihedral_angle_3_deg 10.423 r_dihedral_angle_1_deg 7.139 r_scangle_it 2.703 r_scbond_it 1.955 r_mcangle_it 1.551 r_angle_refined_deg 1.45 r_mcbond_it 0.989 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.234 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.098 r_chiral_restr 0.092 r_symmetry_hbond_refined 0.086 r_bond_refined_d 0.009 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_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 2247 Nucleic Acid Atoms Solvent Atoms 436 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing