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Crystal structure of unknown function protein VPA0057 from Vibrio parahaemolyticus (targeted domain 2-94)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 289 0.1M CaCl2, 0.1M Sodium acetate pH 4.6, 15% PEG 400, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.3 46.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.302 α = 90 b = 37.302 β = 90 c = 135.555 γ = 90
Symmetry Space Group P 43 2 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 2006-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97931 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 1.71 50 99.1 0.075 72 13.4 11162 11064 -3
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 1.71 1.77 93.5 0.352 4.52 9.1 1003
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 1.71 37.29 10480 10480 528 99.45 0.20461 0.20461 0.20298 0.23657 0.2646 RANDOM 26.536
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] 0.41 0.41 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.69 r_dihedral_angle_4_deg 27.031 r_dihedral_angle_3_deg 12.114 r_dihedral_angle_1_deg 7.148 r_scangle_it 3.07 r_scbond_it 2.394 r_angle_refined_deg 1.481 r_mcangle_it 1.293 r_mcbond_it 0.904 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.69 r_dihedral_angle_4_deg 27.031 r_dihedral_angle_3_deg 12.114 r_dihedral_angle_1_deg 7.148 r_scangle_it 3.07 r_scbond_it 2.394 r_angle_refined_deg 1.481 r_mcangle_it 1.293 r_mcbond_it 0.904 r_nbtor_refined 0.301 r_nbd_refined 0.225 r_symmetry_vdw_refined 0.223 r_symmetry_hbond_refined 0.201 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.099 r_bond_refined_d 0.012 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 711 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing