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Putative HopJ type III effector protein from Vibrio parahaemolyticus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QHQ PDB entry 2QHQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 295 0.4M NaH2PO4, 1.6M K2HPO4, 0.1M Imidazole pH 8.0, 0.2M NaCl pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.54 51.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.622 α = 90 b = 90.886 β = 90 c = 72.445 γ = 90
Symmetry Space Group C 2 2 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 CCD ADSC QUANTUM 315 mirrors 2007-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97930 APS 19-ID
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 2.09 50 89 0.111 14.5 10.1 15501 15501
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 2.09 2.18 55.6 0.224 7.2 7.3 958
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 MOLECULAR REPLACEMENT, SAD THROUGHOUT PDB entry 2QHQ 2.09 38.49 13915 13915 1570 88.72 0.217 0.217 0.209 0.209 0.281 0.282 RANDOM 42.718
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] 1.24 -3.92 2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.372 r_dihedral_angle_3_deg 20.209 r_dihedral_angle_4_deg 20.168 r_dihedral_angle_1_deg 6.855 r_scangle_it 4.503 r_scbond_it 3.008 r_angle_refined_deg 1.773 r_mcangle_it 1.584 r_mcbond_it 0.863 r_nbd_refined 0.264
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.372 r_dihedral_angle_3_deg 20.209 r_dihedral_angle_4_deg 20.168 r_dihedral_angle_1_deg 6.855 r_scangle_it 4.503 r_scbond_it 3.008 r_angle_refined_deg 1.773 r_mcangle_it 1.584 r_mcbond_it 0.863 r_nbd_refined 0.264 r_xyhbond_nbd_refined 0.215 r_symmetry_vdw_refined 0.213 r_symmetry_hbond_refined 0.187 r_chiral_restr 0.13 r_metal_ion_refined 0.127 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1855 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing HKL-3000 phasing