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Crystal structure of YopH in complex with 3-(1,1-dioxido-3- oxoisothiazolidin-5-yl)benzaldeyde
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QZ0 PDB ENTRY 1QZ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 MORPHEUS E8 (0.1M BUFFER SYSTEM 2 PH 7.5, 0.12 M ETHYLENE GLYCOLS, 12.5% V/V MPD, 12.5% W/V PEG 3350, , 12.5% W/V PEG 1000)
Crystal Properties Matthews coefficient Solvent content 2.03 39.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.307 α = 90 b = 55.912 β = 90 c = 99.055 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 MARRESEARCH VARIMAX HR-HF 2010-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 1.78 50 95.7 0.05 35.5 6.4 25845 2
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 1.78 1.84 63.4 0.41 2.6 3.4
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 1QZ0 1.79 49.51 24486 1302 96.6 0.17778 0.17589 0.1803 0.21323 0.216 RANDOM 18.758
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] -1.03 0.05 0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.156 r_dihedral_angle_4_deg 15.204 r_dihedral_angle_3_deg 11.912 r_dihedral_angle_1_deg 6.096 r_scangle_it 4.399 r_scbond_it 2.759 r_mcangle_it 1.656 r_angle_refined_deg 1.572 r_angle_other_deg 0.916 r_mcbond_it 0.872
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.156 r_dihedral_angle_4_deg 15.204 r_dihedral_angle_3_deg 11.912 r_dihedral_angle_1_deg 6.096 r_scangle_it 4.399 r_scbond_it 2.759 r_mcangle_it 1.656 r_angle_refined_deg 1.572 r_angle_other_deg 0.916 r_mcbond_it 0.872 r_mcbond_other 0.22 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2166 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction SCALEPACK data scaling MOLREP phasing