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Crystal structure of protein VC0702 from Vibrio cholerae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 PEG 3000, HEPES, NaCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 395K
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.399 α = 90 b = 105.347 β = 104.57 c = 75.272 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 CUSTOM-MADE 2004-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97970 APS 19-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 50 98.4 0.066 21.15 6.2 64372 63342
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 95.2 0.684 1.84 5.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.9 50 60183 59238 3176 98.43 0.18272 0.18272 0.18049 0.1954 0.22552 0.2347 RANDOM 23.13
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] -0.17 0.57 -0.1 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.168 r_dihedral_angle_4_deg 22.916 r_dihedral_angle_3_deg 16.314 r_dihedral_angle_1_deg 5.685 r_scangle_it 4.39 r_scbond_it 3.078 r_mcangle_it 1.573 r_angle_refined_deg 1.481 r_mcbond_it 1.143 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.168 r_dihedral_angle_4_deg 22.916 r_dihedral_angle_3_deg 16.314 r_dihedral_angle_1_deg 5.685 r_scangle_it 4.39 r_scbond_it 3.078 r_mcangle_it 1.573 r_angle_refined_deg 1.481 r_mcbond_it 1.143 r_nbtor_refined 0.305 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.211 r_symmetry_vdw_refined 0.185 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.111 r_bond_refined_d 0.016 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 5428 Nucleic Acid Atoms Solvent Atoms 567 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling HKL-3000 phasing SHELXD phasing SHELXE model building MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing O model building Coot model building CCP4 phasing