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Crystal Structure of S. officinalis PLC21
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZKM PDB code 2ZKM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277.15 100 mM Bis-Tris, 100 mM NaCl, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 2.39 48.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.815 α = 90 b = 89.396 β = 90 c = 163.051 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 110 CCD Rayonix MarMosiac 225 tiled fiber-optic tapers 2009-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.979 APS 21-ID-F
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 1.89 50 97.7 0.069 7.4 3.7 70063 70063 -999999 -2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.92 97.5 3.1
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 (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 code 2ZKM 2 27.36 70063 53335 2826 92.3 0.17754 0.17589 0.1871 0.20819 0.2149 RANDOM 30.916
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.128 r_dihedral_angle_4_deg 14.032 r_dihedral_angle_3_deg 11.666 r_dihedral_angle_1_deg 5.422 r_scangle_it 1.892 r_scbond_it 1.144 r_angle_refined_deg 0.946 r_angle_other_deg 0.743 r_mcangle_it 0.732 r_mcbond_it 0.373
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.128 r_dihedral_angle_4_deg 14.032 r_dihedral_angle_3_deg 11.666 r_dihedral_angle_1_deg 5.422 r_scangle_it 1.892 r_scbond_it 1.144 r_angle_refined_deg 0.946 r_angle_other_deg 0.743 r_mcangle_it 0.732 r_mcbond_it 0.373 r_mcbond_other 0.065 r_chiral_restr 0.057 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 6275 Nucleic Acid Atoms Solvent Atoms 452 Heterogen Atoms 55
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction