☰ Navigation Tabs
Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man-bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DUO PDB ENTRY 2DUO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP & SOAKING 6.5 277 15% PEG4000, 1.5M NaCl, 0.1M MES (pH6.5), 50mM mannose, VAPOR DIFFUSION, HANGING DROP & SOAKING, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.9 57.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.2 α = 90 b = 45 β = 131.9 c = 117 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315 2005-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 1.8 50 96.1 0.099 9.1 3.2 62207 59750 25.1
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) 1.8 1.86 84.5 0.282 2.9 2.6 5173
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2DUO 1.8 20 56615 56615 3022 96.2 0.208 0.208 0.206 0.2045 0.245 0.243 RANDOM 27.49
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] 1.15 1.97 0.18 1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.53 r_dihedral_angle_4_deg 15.693 r_dihedral_angle_3_deg 13.668 r_dihedral_angle_1_deg 6.235 r_scangle_it 2.841 r_scbond_it 1.852 r_angle_refined_deg 1.334 r_mcangle_it 1.286 r_mcbond_it 0.802 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.53 r_dihedral_angle_4_deg 15.693 r_dihedral_angle_3_deg 13.668 r_dihedral_angle_1_deg 6.235 r_scangle_it 2.841 r_scbond_it 1.852 r_angle_refined_deg 1.334 r_mcangle_it 1.286 r_mcbond_it 0.802 r_nbtor_refined 0.305 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.16 r_xyhbond_nbd_refined 0.125 r_symmetry_hbond_refined 0.114 r_chiral_restr 0.092 r_metal_ion_refined 0.077 r_bond_refined_d 0.011 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_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 3974 Nucleic Acid Atoms Solvent Atoms 429 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing