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Crystal Structure Analysis of Plant Exohydrolase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IEQ PDB ENTRY 1IEQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 75mM HEPES-NaOH pH7.0 buffer, 1.2% PEG 400, 1.7M ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.57 65.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.015 α = 90 b = 101.015 β = 90 c = 182.06 γ = 90
Symmetry Space Group P 43 21 2
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 QUANTUM 315 collimating mirror, double-crystal Si(111) monochromator 2007-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 1.65 31.94 98.5 0.089 1 13 106290 106290 1
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 1IEQ 1.65 31.94 106290 5636 98.48 0.16244 0.1608 0.1573 0.19294 0.1892 RANDOM 26.486
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] -0.32 -0.32 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.961 r_dihedral_angle_4_deg 14.786 r_dihedral_angle_3_deg 12.496 r_sphericity_bonded 9.059 r_sphericity_free 8.469 r_dihedral_angle_1_deg 5.952 r_scangle_it 4.15 r_scbond_it 2.988 r_mcangle_it 2.066 r_rigid_bond_restr 1.776
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.961 r_dihedral_angle_4_deg 14.786 r_dihedral_angle_3_deg 12.496 r_sphericity_bonded 9.059 r_sphericity_free 8.469 r_dihedral_angle_1_deg 5.952 r_scangle_it 4.15 r_scbond_it 2.988 r_mcangle_it 2.066 r_rigid_bond_restr 1.776 r_angle_refined_deg 1.583 r_mcbond_it 1.46 r_nbtor_refined 0.311 r_symmetry_hbond_refined 0.227 r_symmetry_vdw_refined 0.213 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.121 r_bond_refined_d 0.018 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4566 Nucleic Acid Atoms Solvent Atoms 838 Heterogen Atoms 218
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling