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Structure of the hypothetical protein VC0508 from Vibrio cholerae VSP- II pathogenicity island
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V1L PDB ENTRY 2V1L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 PH 5.5
Crystal Properties Matthews coefficient Solvent content 2.05 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.102 α = 90 b = 70.596 β = 110.64 c = 51.382 γ = 90
Symmetry Space Group P 1 21 1
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 RIGAKU SATURN 944 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 1.9 20 97 0.03 62 6.5 21026
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 1.9 1.97 96 0.03 5.6 6.2
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 2V1L 1.9 48.06 19870 1065 96.4 0.227 0.224 0.224 0.275 0.2765 RANDOM 36.22
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] 0.56 0.57 0.64 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.21 r_dihedral_angle_4_deg 16.628 r_dihedral_angle_3_deg 15.125 r_dihedral_angle_1_deg 5.542 r_scangle_it 3.299 r_scbond_it 2.122 r_mcangle_it 1.491 r_angle_refined_deg 1.339 r_mcbond_it 0.901 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.21 r_dihedral_angle_4_deg 16.628 r_dihedral_angle_3_deg 15.125 r_dihedral_angle_1_deg 5.542 r_scangle_it 3.299 r_scbond_it 2.122 r_mcangle_it 1.491 r_angle_refined_deg 1.339 r_mcbond_it 0.901 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.224 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.096 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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_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 2247 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing