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Crystal structure of Gamma-glutamylcysteine synthetase from Escherichia Coli B complexed with Transition-state analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V4G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 PEG 2000MME, MgCl2, Tris-HCl buffer, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.78 55.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.468 α = 90 b = 97.36 β = 109.63 c = 102.185 γ = 90
Symmetry Space Group P 1 21 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 CCD MARRESEARCH 2003-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.1 48.8 97.2 0.084 14.8 4.8 73644 73622
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) 2.1 2.15 96.3 0.379 3.5 4.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1V4G 2.1 40 69912 3702 97.02 0.2 0.2 0.2251 0.225 0.2437 RANDOM 27.31
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] -2.5 -2.32 0.64 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.009 r_mcangle_it 4.422 r_scangle_it 4.374 r_angle_other_deg 3.658 r_scbond_it 3.096 r_mcbond_it 3.073 r_angle_refined_deg 1.344 r_symmetry_vdw_other 0.351 r_nbd_other 0.29 r_nbd_refined 0.215
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.009 r_mcangle_it 4.422 r_scangle_it 4.374 r_angle_other_deg 3.658 r_scbond_it 3.096 r_mcbond_it 3.073 r_angle_refined_deg 1.344 r_symmetry_vdw_other 0.351 r_nbd_other 0.29 r_nbd_refined 0.215 r_symmetry_hbond_refined 0.199 r_xyhbond_nbd_refined 0.198 r_symmetry_vdw_refined 0.196 r_metal_ion_refined 0.15 r_nbtor_other 0.116 r_chiral_restr 0.082 r_bond_refined_d 0.018 r_gen_planes_other 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7998 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 142
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing