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Crystal structure of aspartic proteinase from Irpex lacteus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PEP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 293 50% saturated ammonium phosphate, 10mM sodium citrate-sulfate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.31 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.27 α = 90 b = 78.898 β = 96.71 c = 54.072 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 100 AREA DETECTOR MARRESEARCH 2001-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 1.3 50 99.1 0.037 25.4 5 77021 75525 8.6
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 1.3 1.35 98.3 0.222 4.9 4.7 7488
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4pep 1.3 26.99 75485 3789 98.8 0.147 0.147 0.1552 0.171 0.1781 RANDOM 10.1
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] -0.07 0.42 -0.13 0.2
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.9 c_improper_angle_d 3.01 c_scangle_it 2.35 c_angle_deg 2.3 c_scbond_it 1.94 c_mcangle_it 1.21 c_mcbond_it 0.91 c_bond_d 0.034 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.9 c_improper_angle_d 3.01 c_scangle_it 2.35 c_angle_deg 2.3 c_scbond_it 1.94 c_mcangle_it 1.21 c_mcbond_it 0.91 c_bond_d 0.034 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 2520 Nucleic Acid Atoms Solvent Atoms 702 Heterogen Atoms 35
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing