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NATIVE CARDOSIN A FROM CYNARA CARDUNCULUS L.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LYB HUMAN CATHEPSIN D (PDB ENTRY 1LYB))
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 LYOPHILIZED PROTEIN DISSOLVED IN WATER TO 12 MG/ML, SITTING DROPS OF PROTEIN SOLUTION AN ALIQUOTA OF PRECIPITANT SOLUTION, COMPOSED OF PEG 4 K 40%, SODIUM CITRATE BUFFER 0.1 M AND AMMONIUM ACETATE 0.2 M, pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.26 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.964 α = 90 b = 87.186 β = 104.43 c = 81.303 γ = 90
Symmetry Space Group C 1 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 IMAGE PLATE MARRESEARCH 1997-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 1.72 34.78 96.9 0.062 15.9 11.3 84399
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 1.72 1.75 99.3 0.413 2.5 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R HUMAN CATHEPSIN D (PDB ENTRY 1LYB)) 1.72 34.8 83681 3994 99.8 0.206 0.205 0.1955 0.256 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 18 4964 5754.5
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.069 s_non_zero_chiral_vol 0.045 s_similar_dist 0.04 s_zero_chiral_vol 0.038 s_from_restr_planes 0.03 s_angle_d 0.025 s_anti_bump_dis_restr 0.021 s_bond_d 0.007 s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5000 Nucleic Acid Atoms Solvent Atoms 528 Heterogen Atoms 229
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing SHELXL-97 refinement