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Glutamyl endopeptidase from Bacillus intermedius
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AGJ PDB ENTRY 1AGJ
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, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.06 39.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.494 α = 90 b = 85.437 β = 90 c = 82.147 γ = 90
Symmetry Space Group C 2 2 21
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 1999-01-15 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 1.5 19.5 97.3 33771 33011 -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 1.5 1.54 95.7
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 1AGJ 1.5 19.32 -2 33771 33010 1132 97.56 0.158 0.156 0.153 0.1519 0.184 0.1523 random 14.392
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] -0.67 0.19 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.388 r_scangle_it 4.216 r_scbond_it 2.574 r_mcangle_it 1.718 r_angle_refined_deg 1.43 r_mcbond_it 0.914 r_angle_other_deg 0.826 r_symmetry_hbond_refined 0.381 r_symmetry_vdw_other 0.307 r_nbd_other 0.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.388 r_scangle_it 4.216 r_scbond_it 2.574 r_mcangle_it 1.718 r_angle_refined_deg 1.43 r_mcbond_it 0.914 r_angle_other_deg 0.826 r_symmetry_hbond_refined 0.381 r_symmetry_vdw_other 0.307 r_nbd_other 0.247 r_xyhbond_nbd_refined 0.206 r_nbd_refined 0.186 r_symmetry_vdw_refined 0.099 r_chiral_restr 0.097 r_nbtor_other 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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 155 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing