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Crystal structure of Bacillus subtilis gamma-glutamyltranspeptidase in complex with acivicin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A75
Crystallization Crystal Properties Matthews coefficient Solvent content 2.34 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.075 α = 90 b = 71.666 β = 90 c = 144.357 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 2011-09-10 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 1.8 50 96.8 56723 56723
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 1.8 1.86 92.6 0.396
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3A75 1.8 30.04 53749 53749 2883 96.82 0.18411 0.18411 0.18274 0.20911 0.2218 RANDOM 23.966
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 38.95 r_dihedral_angle_4_deg 14.832 r_dihedral_angle_3_deg 14.185 r_dihedral_angle_1_deg 6.122 r_scangle_it 3.456 r_scbond_it 2.165 r_angle_refined_deg 1.391 r_mcangle_it 1.307 r_mcbond_it 0.792 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.95 r_dihedral_angle_4_deg 14.832 r_dihedral_angle_3_deg 14.185 r_dihedral_angle_1_deg 6.122 r_scangle_it 3.456 r_scbond_it 2.165 r_angle_refined_deg 1.391 r_mcangle_it 1.307 r_mcbond_it 0.792 r_nbtor_refined 0.307 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.193 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.113 r_symmetry_hbond_refined 0.11 r_bond_refined_d 0.013 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 291 Heterogen Atoms 10
Software Software Software Name Purpose BSS data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling