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Crystal Structure of the 4-Oxalocrotonate Tautomerase Homologue DmpI from Helicobacter pylori.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BJP PDB ENTRY 1BJP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 277 2 uL of protein (20 mg/mL) in 20mM phosphate buffer (pH 7.4) were mixed with 2 uL of 0.2M CaCl2, 0.1M Hepes (pH 7.5), and 28% PEG 400. This combined volume was equilibrated at 4 degrees Celcius against 50 uL of 0.2M CaCl2, 0.1M Hepes (pH 7.5), and 28% PEG 400 , VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.11 41.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.83 α = 90 b = 50.77 β = 99.13 c = 89.31 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 108 IMAGE PLATE RIGAKU RAXIS IV 2000-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 2.1 24.5 90 0.096 13.5 5.94 20368 19.2
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 2.1 2.18 90 0.476 4
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 (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 RANDOM PDB ENTRY 1BJP 2.1 24.5 21823 20368 1044 92.1 0.217 0.217 0.2164 0.249 0.2516 THROUGHOUT 31
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] 1.99 0.85 -2.06 0.07
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.5 c_angle_deg 1.1 c_improper_angle_d 0.77 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.5 c_angle_deg 1.1 c_improper_angle_d 0.77 c_bond_d 0.007 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 c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2932 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing CNS refinement DENZO data reduction SCALEPACK data scaling