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Crystal structure of gamma-glutamyl hydrolase (C108A) complex with MTX
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L9X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 20% PEG 8000, 0.1M Tris, 0.2M Magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.23 44.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.396 α = 90 b = 198.098 β = 113.816 c = 65.112 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 110 CCD ADSC QUANTUM 315 2012-01-10 M SINGLE WAVELENGTH 2 1 x-ray 110 CCD ADSC QUANTUM 315r 2012-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1 2 SYNCHROTRON NSRRC BEAMLINE BL13C1 1.0 NSRRC BL13C1
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 1,2 1.97 30 99 81489 81489
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 1.97 2.04 99.3
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 (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 1L9X 1.97 30 91616 81489 4309 99.23 0.17799 0.17474 0.1773 0.23857 0.2368 RANDOM 20.95
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 38.558 r_dihedral_angle_4_deg 22.753 r_dihedral_angle_3_deg 17.276 r_dihedral_angle_1_deg 6.466 r_scangle_it 5.384 r_scbond_it 3.443 r_mcangle_it 2.196 r_angle_refined_deg 1.982 r_mcbond_it 1.245 r_chiral_restr 0.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.558 r_dihedral_angle_4_deg 22.753 r_dihedral_angle_3_deg 17.276 r_dihedral_angle_1_deg 6.466 r_scangle_it 5.384 r_scbond_it 3.443 r_mcangle_it 2.196 r_angle_refined_deg 1.982 r_mcbond_it 1.245 r_chiral_restr 0.207 r_bond_refined_d 0.024 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9232 Nucleic Acid Atoms Solvent Atoms 953 Heterogen Atoms 66
Software Software Software Name Purpose ADSC data collection X-PLOR model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling X-PLOR phasing