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Crystal structure of human IPP isomerase I in space group P212121
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.4M MnCl2, 0.1M Sodium Cacodylate PH6.5, 20% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.35 47.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.019 α = 90 b = 62.947 β = 90 c = 74.188 γ = 90
Symmetry Space Group P 21 21 21
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 2005-04-14 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 1.6 50 96.3 0.069 16.8 10.5 33566
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) 1.6 1.66 68.7 0.373 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.6 25.79 33512 1694 96.29 0.175 0.173 0.1855 0.203 0.2098 RANDOM 18.506
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] 1.11 -0.63 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.967 r_dihedral_angle_4_deg 15.697 r_dihedral_angle_3_deg 11.783 r_dihedral_angle_1_deg 5.84 r_scangle_it 1.927 r_scbond_it 1.258 r_angle_refined_deg 1.114 r_mcangle_it 0.743 r_mcbond_it 0.386 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.967 r_dihedral_angle_4_deg 15.697 r_dihedral_angle_3_deg 11.783 r_dihedral_angle_1_deg 5.84 r_scangle_it 1.927 r_scbond_it 1.258 r_angle_refined_deg 1.114 r_mcangle_it 0.743 r_mcbond_it 0.386 r_nbtor_refined 0.305 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.187 r_xyhbond_nbd_refined 0.105 r_symmetry_hbond_refined 0.101 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1818 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 20
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data reduction HKL-2000 data scaling SHARP phasing