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Structure of Glu endopeptidase in complex with MPD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P3C PDB ENTRY 1P3C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 0.01 M Tris-HCl buffer, pH 7.0, 2 mM CaCl2, 1.2 M potassium phosphate, 3% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.85 33.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.936 α = 90 b = 55.757 β = 118.17 c = 60.195 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 1999-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 1.10 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 20 93 18778 18778 -2 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.76 95.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1P3C 1.72 19.69 -3 17769 17769 965 97.34 0.16791 0.16791 0.16579 0.1745 0.20809 0.2116 RANDOM 13.378
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] 0.84 1.84 -0.23 1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.782 r_scangle_it 3.734 r_scbond_it 2.301 r_mcangle_it 1.557 r_angle_refined_deg 1.42 r_angle_other_deg 1.191 r_mcbond_it 0.877 r_symmetry_vdw_other 0.361 r_symmetry_hbond_refined 0.275 r_nbd_other 0.245
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.782 r_scangle_it 3.734 r_scbond_it 2.301 r_mcangle_it 1.557 r_angle_refined_deg 1.42 r_angle_other_deg 1.191 r_mcbond_it 0.877 r_symmetry_vdw_other 0.361 r_symmetry_hbond_refined 0.275 r_nbd_other 0.245 r_symmetry_vdw_refined 0.226 r_nbd_refined 0.183 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.121 r_nbtor_other 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1600 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing