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Crystal structures of transition state analogue inhibitors of inosine monophosphate cyclohydrolase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G8M PDB entry 1G8M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 295 PEG 8000, imidazole, DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.6 52.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.2 α = 80.8 b = 62 β = 81.5 c = 196.6 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD ADSC 2004-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1271 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 50 83.6 0.06 11.4 1.6 131382 118497 38.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 42.2 42.2 0.351 1.3 1.2 3334
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 PDB entry 1G8M 2.1 41.89 131382 118496 2967 93.85 0.2 0.243 0.199 0.1984 0.248 0.2489 RANDOM 42.044
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] 0.7 -0.16 0.04 -0.71 0.25 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.053 r_dihedral_angle_3_deg 16.83 r_dihedral_angle_4_deg 16.311 r_dihedral_angle_1_deg 5.601 r_scangle_it 2.647 r_scbond_it 1.671 r_angle_refined_deg 1.334 r_mcangle_it 0.963 r_mcbond_it 0.516 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.053 r_dihedral_angle_3_deg 16.83 r_dihedral_angle_4_deg 16.311 r_dihedral_angle_1_deg 5.601 r_scangle_it 2.647 r_scbond_it 1.671 r_angle_refined_deg 1.334 r_mcangle_it 0.963 r_mcbond_it 0.516 r_nbtor_refined 0.3 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.172 r_xyhbond_nbd_refined 0.138 r_symmetry_hbond_refined 0.134 r_metal_ion_refined 0.133 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18044 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms 56
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction