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X-Ray Structure of the C-terminal domain (277-440) of Putative chitobiase from Bacteroides thetaiotaomicron. Northeast Structural Genomics Consortium Target BtR324A.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F2Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.75M MgFormate, 0.1M Bis-Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.96 58.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.86 α = 90 b = 86.86 β = 90 c = 50.992 γ = 120
Symmetry Space Group P 32 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 CCD ADSC QUANTUM 4 mirrors 2009-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.979 NSLS X4A
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 3 50 99.9 0.085 9.4 8624 -3
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) 3 3.11 100 0.484 8.6
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 3F2Z 3 20 4615 210 100 0.202 0.2 0.2517 0.251 0.3015 RANDOM 66.961
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] -0.16 -0.08 -0.16 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.433 r_dihedral_angle_3_deg 19.331 r_dihedral_angle_4_deg 15.843 r_dihedral_angle_1_deg 6.632 r_angle_refined_deg 1.384 r_scangle_it 1.142 r_scbond_it 0.653 r_mcangle_it 0.506 r_nbtor_refined 0.324 r_mcbond_it 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.433 r_dihedral_angle_3_deg 19.331 r_dihedral_angle_4_deg 15.843 r_dihedral_angle_1_deg 6.632 r_angle_refined_deg 1.384 r_scangle_it 1.142 r_scbond_it 0.653 r_mcangle_it 0.506 r_nbtor_refined 0.324 r_mcbond_it 0.304 r_symmetry_vdw_refined 0.262 r_nbd_refined 0.238 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.099 r_symmetry_hbond_refined 0.027 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1243 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction SCALEPACK data scaling BALBES phasing