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Crystal structure of human type I IPP isomerase complexed with a substrate analog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DHO PDB ENTRY 2DHO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.2M Magnesium Acetate, 0.1M Sodium Cacodylate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.07 40.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.363 α = 80.26 b = 43.074 β = 89.98 c = 70.466 γ = 67.95
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 RAXIS IV 2005-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 50 94.1 0.098 9.5 5.5 28398
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 2.07 87 0.464 5.2
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 PDB ENTRY 2DHO 2 20.4 26831 1417 94.28 0.22238 0.22023 0.2299 0.26182 0.2777 RANDOM 40.404
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] -0.73 -2.65 0.36 6.03 -0.91 -3.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.663 r_sphericity_free 26.387 r_dihedral_angle_4_deg 17.999 r_dihedral_angle_3_deg 15.591 r_dihedral_angle_1_deg 6.199 r_scangle_it 3.45 r_sphericity_bonded 3.341 r_scbond_it 2.379 r_rigid_bond_restr 1.64 r_mcangle_it 1.557
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.663 r_sphericity_free 26.387 r_dihedral_angle_4_deg 17.999 r_dihedral_angle_3_deg 15.591 r_dihedral_angle_1_deg 6.199 r_scangle_it 3.45 r_sphericity_bonded 3.341 r_scbond_it 2.379 r_rigid_bond_restr 1.64 r_mcangle_it 1.557 r_angle_refined_deg 1.293 r_mcbond_it 0.991 r_nbtor_refined 0.301 r_nbd_refined 0.223 r_symmetry_hbond_refined 0.182 r_xyhbond_nbd_refined 0.163 r_symmetry_vdw_refined 0.145 r_metal_ion_refined 0.128 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3649 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 30
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction MOLREP phasing