☰ Navigation Tabs
Crystal structure of gamma-glutamyltranspeptidase from Bacillus subtilis (crystal soaked for 0 min. in acivicin soln. )
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V36
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Oil batch 7 293 26% (w/v) PEG 3350, 0.7M sodium thiocyanate, 6% (v/v) ethylene glycol, pH 7.0, Oil batch, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 46.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.633 α = 90 b = 71.664 β = 90 c = 143.746 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC QUANTUM 315 2010-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.000 SPring-8 BL38B1
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 1.85 50 99.9 53570 1 1
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 1.85 1.92 100 0.339
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 2V36 1.85 28.7 1 50760 50760 2716 99.73 0.17784 0.17784 0.17598 0.1783 0.21351 0.2142 RANDOM 20.019
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] -0.05 0.03 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.612 r_dihedral_angle_4_deg 16.067 r_dihedral_angle_3_deg 14.227 r_dihedral_angle_1_deg 6.349 r_scangle_it 3.575 r_scbond_it 2.284 r_angle_refined_deg 1.417 r_mcangle_it 1.352 r_mcbond_it 0.839 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.612 r_dihedral_angle_4_deg 16.067 r_dihedral_angle_3_deg 14.227 r_dihedral_angle_1_deg 6.349 r_scangle_it 3.575 r_scbond_it 2.284 r_angle_refined_deg 1.417 r_mcangle_it 1.352 r_mcbond_it 0.839 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.22 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.178 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.117 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4185 Nucleic Acid Atoms Solvent Atoms 458 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling