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Crystal Structure of a GH7 Family Cellobiohydrolase from Daphnia pulex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YG1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 289 800mM ammonium sulphate, 100mM sodium citrate, 10mM sodium acetate, 50mM sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.58 52.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.29 α = 90 b = 47.02 β = 108.23 c = 173.5 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 PIXEL PSI PILATUS 6M 2014-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.9 43.6 90 0.065 0.091 7.85 1.76 75459 -3 34.459
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 91 0.584 0.826 1.46
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 2YG1 1.9 43.6 71506 3640 96.14 0.166 0.1637 0.173 0.2095 0.2154 RANDOM 31.657
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] -0.13 -0.18 -0.21 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.811 r_dihedral_angle_4_deg 23.484 r_dihedral_angle_3_deg 15.058 r_dihedral_angle_1_deg 6.718 r_mcangle_it 2.833 r_mcbond_it 2.069 r_mcbond_other 2.067 r_angle_refined_deg 1.876 r_angle_other_deg 0.934 r_chiral_restr 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.811 r_dihedral_angle_4_deg 23.484 r_dihedral_angle_3_deg 15.058 r_dihedral_angle_1_deg 6.718 r_mcangle_it 2.833 r_mcbond_it 2.069 r_mcbond_other 2.067 r_angle_refined_deg 1.876 r_angle_other_deg 0.934 r_chiral_restr 0.13 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6752 Nucleic Acid Atoms Solvent Atoms 543 Heterogen Atoms 12
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction