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Crystal structure of a meta-cleavage product hydrolase (CumD) complexed with benzoate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IUP PDB ENTRY 1IUP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.1 283 PEG4000, AMMONIUM benzoate, SODIUM benzoate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.49 50.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.596 α = 90 b = 116.181 β = 90 c = 78.848 γ = 90
Symmetry Space Group C 2 2 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 QUANTUM 4 2002-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B 1.000 Photon Factory BL-18B
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 1.8 25.994 100 0.068 6.8 3.6 32970 32962 10.9
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) 1.8 1.9 99.9 0.259 3
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 (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1IUP 1.8 25.99 32962 32942 1640 99.8 0.172 0.171 0.171 0.1722 0.199 0.1752 RANDOM 14.5
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] 1.11 -0.85 -0.26
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.4 c_scangle_it 5.19 c_scbond_it 3.73 c_mcangle_it 2.61 c_mcbond_it 2.08 c_angle_deg 1.3 c_improper_angle_d 0.72 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.4 c_scangle_it 5.19 c_scbond_it 3.73 c_mcangle_it 2.61 c_mcbond_it 2.08 c_angle_deg 1.3 c_improper_angle_d 0.72 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2139 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 27
Software Software Software Name Purpose CNS refinement MOSFLM data reduction CCP4 data scaling CNS phasing