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Effect of Dimethyl Sulphoxide on the crystal structure of Porcine Pepsin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5PEP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SLOW COOLING 3.6 300 sulphuric acid, pH 3.6, SLOW COOLING, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.6 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.47 α = 90 b = 67.47 β = 90 c = 290.294 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 300 IMAGE PLATE MARRESEARCH osmic mirrors 2003-12-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3 20 0.076 0.076 25.2 8624 8077
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3 3.1 91.1 0.176 0.176 14.25
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 THROUGHOUT 5PEP 3 18.37 8554 7706 829 90.1 0.186 0.186 0.1871 0.28 0.2801 RANDOM 44.6
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] 2.46 13.03 2.46 -4.92
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.5 c_mcangle_it 4.06 c_scangle_it 3.46 c_mcbond_it 2.3 c_scbond_it 2.13 c_angle_deg 1.3 c_improper_angle_d 0.79 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.5 c_mcangle_it 4.06 c_scangle_it 3.46 c_mcbond_it 2.3 c_scbond_it 2.13 c_angle_deg 1.3 c_improper_angle_d 0.79 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 2429 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 4
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing