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Crystal structure of the domain of putative sensory box/GGDEF family protein from Vibrio parahaemolyticus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 0.2M LiSO4, 25% PEG 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.73 54.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.98 α = 90 b = 81.596 β = 90 c = 121.851 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 CCD ADSC QUANTUM 315 2007-02-04 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 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 2.25 50 99.8 0.11 32.2 9 34928 33442 2 43
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 2.25 2.33 100 0.583 3.96 8.8 3433
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.25 38.69 33090 33090 1746 98.97 0.19577 0.19577 0.19346 0.23863 0.2342 RANDOM 42.187
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] 1.64 0.81 -2.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.487 r_dihedral_angle_4_deg 19.239 r_dihedral_angle_3_deg 14.415 r_dihedral_angle_1_deg 11.55 r_scangle_it 3.484 r_scbond_it 2.154 r_angle_refined_deg 1.544 r_mcangle_it 1.378 r_mcbond_it 0.709 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.487 r_dihedral_angle_4_deg 19.239 r_dihedral_angle_3_deg 14.415 r_dihedral_angle_1_deg 11.55 r_scangle_it 3.484 r_scbond_it 2.154 r_angle_refined_deg 1.544 r_mcangle_it 1.378 r_mcbond_it 0.709 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.28 r_symmetry_vdw_refined 0.248 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.189 r_chiral_restr 0.115 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined 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 4391 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing