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Crystal structure of Inosine-5'-monophosphate dehydrogenase (TM1347) from THERMOTOGA MARITIMA at 2.18 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZFJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 4 273 40% MPD, 0.1M citric acid pH 4.0, final pH 4, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 3.8 67.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.083 α = 90 b = 120.083 β = 90 c = 144.079 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 100 CCD ADSC 2001-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 ALS 5.0.3
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 2.18 46.12 94.49 0.078 14.26 4.11 50043 44.79
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 2.18 2.2 75.52 0.574 1.51 3.26 1308
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 1zfj 2.18 46.12 47472 2553 94.22 0.21863 0.21653 0.2178 0.25759 0.2582 RANDOM 39.358
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] -2.2 -2.2 4.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.071 r_dihedral_angle_4_deg 16.725 r_dihedral_angle_3_deg 15.276 r_scangle_it 8.37 r_scbond_it 6.057 r_dihedral_angle_1_deg 5.935 r_mcangle_it 3.083 r_mcbond_it 2.073 r_angle_refined_deg 1.523 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.071 r_dihedral_angle_4_deg 16.725 r_dihedral_angle_3_deg 15.276 r_scangle_it 8.37 r_scbond_it 6.057 r_dihedral_angle_1_deg 5.935 r_mcangle_it 3.083 r_mcbond_it 2.073 r_angle_refined_deg 1.523 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.215 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.188 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4670 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement