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Crystal structure of gamma-glutamyltranspeptidase from Bacillus subtilis (crystal soaked for 3min. in acivicin soln. )
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A75
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 2.27 45.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.786 α = 90 b = 71.802 β = 90 c = 142.416 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 2010-06-23 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 1.58 50 98.1 81531 81531
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 1.58 1.64 97.8 0.17
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3A75 1.58 23.22 77308 77308 4095 98.07 0.16835 0.16835 0.16751 0.169 0.18404 0.1837 RANDOM 15.338
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 37.384 r_dihedral_angle_4_deg 15.172 r_dihedral_angle_3_deg 12.98 r_dihedral_angle_1_deg 5.952 r_scangle_it 3.043 r_scbond_it 1.921 r_angle_refined_deg 1.203 r_mcangle_it 1.079 r_mcbond_it 0.653 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.384 r_dihedral_angle_4_deg 15.172 r_dihedral_angle_3_deg 12.98 r_dihedral_angle_1_deg 5.952 r_scangle_it 3.043 r_scbond_it 1.921 r_angle_refined_deg 1.203 r_mcangle_it 1.079 r_mcbond_it 0.653 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.205 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.152 r_symmetry_hbond_refined 0.148 r_chiral_restr 0.101 r_bond_refined_d 0.008 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 4165 Nucleic Acid Atoms Solvent Atoms 505 Heterogen Atoms
Software Software Software Name Purpose BSS data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling