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Crystal structure of protein VC1974 from Vibrio cholerae, Pfam abhydrolase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 32% PEG 4000, .1M Tris pH 8.0, 10% Isopropanol, .24M Na Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.47 α = 90 b = 99.47 β = 90 c = 53.492 γ = 90
Symmetry Space Group P 42 21 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 2003-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 8-BM .978 APS 8-BM
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 1.9 20 0.089 18.3 21381 21381 -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) 1.9 1.97 99.5 0.41 6.5
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.9 20 21357 20222 1089 98.25 0.18108 0.17932 0.1922 0.21554 0.2352 RANDOM 27.27
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] 0.49 0.49 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.752 r_dihedral_angle_4_deg 20.881 r_dihedral_angle_3_deg 14.429 r_dihedral_angle_1_deg 5.82 r_scangle_it 4.48 r_scbond_it 3.061 r_mcangle_it 1.74 r_angle_refined_deg 1.439 r_mcbond_it 1.385 r_angle_other_deg 0.829
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.752 r_dihedral_angle_4_deg 20.881 r_dihedral_angle_3_deg 14.429 r_dihedral_angle_1_deg 5.82 r_scangle_it 4.48 r_scbond_it 3.061 r_mcangle_it 1.74 r_angle_refined_deg 1.439 r_mcbond_it 1.385 r_angle_other_deg 0.829 r_mcbond_other 0.276 r_symmetry_vdw_other 0.249 r_nbd_refined 0.234 r_nbd_other 0.19 r_symmetry_vdw_refined 0.186 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.141 r_symmetry_hbond_refined 0.136 r_chiral_restr 0.09 r_nbtor_other 0.088 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1985 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing