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Crystal Structure of Michaelis Complex of gamma-Glutamylcysteine Synthetase
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 sodium formate, Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.77 74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 325.53 α = 90 b = 325.53 β = 90 c = 105.003 γ = 120
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 RIGAKU 2005-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.9000 SPring-8 BL38B1
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 2.4 43.6 100 0.088 6.1 8.1 162223 50.5
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) 2.4 2.53 100 0.374 2 7.9 23722
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 2.4 40 154095 8122 0.16994 0.16841 0.1789 0.19844 0.2084 RANDOM 45.908
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] 0.14 0.07 0.14 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.55 r_dihedral_angle_4_deg 19.299 r_dihedral_angle_3_deg 15.266 r_dihedral_angle_1_deg 5.589 r_scangle_it 2.584 r_mcangle_it 2.376 r_scbond_it 1.869 r_mcbond_it 1.548 r_angle_refined_deg 1.381 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.55 r_dihedral_angle_4_deg 19.299 r_dihedral_angle_3_deg 15.266 r_dihedral_angle_1_deg 5.589 r_scangle_it 2.584 r_mcangle_it 2.376 r_scbond_it 1.869 r_mcbond_it 1.548 r_angle_refined_deg 1.381 r_nbtor_refined 0.317 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.166 r_xyhbond_nbd_refined 0.157 r_symmetry_hbond_refined 0.156 r_chiral_restr 0.086 r_metal_ion_refined 0.042 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15828 Nucleic Acid Atoms Solvent Atoms 800 Heterogen Atoms 205
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing