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Crystal structure of iminodisuccinate epimerase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HP0 PDB entry 2HP0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.2 298 22 % PEG 3350, 0.2M ammonium sulphate, 0.1M Bis-Tris propane, pH 7.2, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.31 46.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.365 α = 90 b = 104.21 β = 103.33 c = 78.545 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 100 CCD MAR CCD 165 mm 2005-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.0628 MAX II I711
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 1.7 23 97.6 0.069 14.3 92811 92811
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) 1.7 1.79 84.5 0.29 3.4
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 MIR THROUGHOUT PDB entry 2HP0 1.71 23 93881 92783 4680 98.78 0.15893 0.15893 0.15718 0.1696 0.19155 0.201 RANDOM 13.324
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] 0.13 -0.24 0.91 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.491 r_dihedral_angle_4_deg 15.286 r_dihedral_angle_3_deg 12.391 r_dihedral_angle_1_deg 5.57 r_scangle_it 2.803 r_scbond_it 1.921 r_angle_refined_deg 1.364 r_mcangle_it 1.102 r_mcbond_it 0.932 r_angle_other_deg 0.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.491 r_dihedral_angle_4_deg 15.286 r_dihedral_angle_3_deg 12.391 r_dihedral_angle_1_deg 5.57 r_scangle_it 2.803 r_scbond_it 1.921 r_angle_refined_deg 1.364 r_mcangle_it 1.102 r_mcbond_it 0.932 r_angle_other_deg 0.828 r_symmetry_vdw_other 0.234 r_nbd_refined 0.216 r_mcbond_other 0.208 r_symmetry_vdw_refined 0.185 r_nbd_other 0.184 r_nbtor_refined 0.178 r_symmetry_hbond_refined 0.138 r_xyhbond_nbd_refined 0.134 r_nbtor_other 0.087 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_xyhbond_nbd_other 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6852 Nucleic Acid Atoms Solvent Atoms 719 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing