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CcCel6C, a glycoside hydrolase family 6 enzyme, complexed with p-nitrophenyl beta-D-cellotrioside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A64 PDB ENTRY 3A64
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 30% PEG 8000, 0.1M HEPES-KOH, 0.15M magnesium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.03 39.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.876 α = 77.63 b = 45.153 β = 86.87 c = 48.989 γ = 68.8
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 210 2008-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 1.4 50 94.8 0.064 25.7 2 63990 63990
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) 1.4 1.45 90.6 0.175 3.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3A64 1.4 24.89 57526 6456 94.7 0.16599 0.1634 0.18875 0.1887 RANDOM 14.802
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] -0.03 0.02 0.01 0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.619 r_dihedral_angle_4_deg 19.473 r_dihedral_angle_3_deg 11.967 r_dihedral_angle_1_deg 5.58 r_scangle_it 2.555 r_scbond_it 1.746 r_angle_refined_deg 1.219 r_mcangle_it 1.057 r_mcbond_it 0.585 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.619 r_dihedral_angle_4_deg 19.473 r_dihedral_angle_3_deg 11.967 r_dihedral_angle_1_deg 5.58 r_scangle_it 2.555 r_scbond_it 1.746 r_angle_refined_deg 1.219 r_mcangle_it 1.057 r_mcbond_it 0.585 r_nbtor_refined 0.315 r_symmetry_vdw_refined 0.203 r_nbd_refined 0.201 r_symmetry_hbond_refined 0.134 r_xyhbond_nbd_refined 0.102 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 2940 Nucleic Acid Atoms Solvent Atoms 494 Heterogen Atoms 65
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling