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Structure of prolyl endoprotease from Aspergillus niger CBS 109712
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other composite model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 26-29% (w/v) PEG 3350, 0.1 M sodium citrate pH 5.0, 0.1 M ammonium tartrate pH 7.2, 20 mM HAc/NaAc pH 5.0, 50 mM NaCl
Crystal Properties Matthews coefficient Solvent content 3.27 62.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.03 α = 90 b = 162.03 β = 90 c = 162.03 γ = 90
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 315r 2009-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9195 ESRF ID14-4
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 2.42 66.24 100 0.108 14.5 9.2 27027
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 2.42 2.55 99.9 0.636 3.7 9.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT composite model 2.42 66.24 25707 1335 99.94 0.17151 0.16956 0.20892 0.1897 RANDOM 42.924
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.027 r_dihedral_angle_4_deg 19.125 r_dihedral_angle_3_deg 14.342 r_dihedral_angle_1_deg 5.916 r_long_range_B_refined 5.761 r_long_range_B_other 5.753 r_scangle_other 4.726 r_scbond_it 3.305 r_scbond_other 3.305 r_mcangle_it 2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.027 r_dihedral_angle_4_deg 19.125 r_dihedral_angle_3_deg 14.342 r_dihedral_angle_1_deg 5.916 r_long_range_B_refined 5.761 r_long_range_B_other 5.753 r_scangle_other 4.726 r_scbond_it 3.305 r_scbond_other 3.305 r_mcangle_it 2.26 r_mcangle_other 2.26 r_mcbond_it 1.474 r_mcbond_other 1.474 r_angle_refined_deg 1.403 r_angle_other_deg 1.1 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3845 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 301
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MR-Rosetta phasing