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Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man2-bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DUQ PDB ENTRY 2DUQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 5% PEG4000, 0.3M MgCl2, 3.4mM mannobiose, 0.1M MES (pH 6.5), VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.9 57.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.2 α = 90 b = 45.5 β = 132.7 c = 117.4 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 2006-02-01 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 1.65 50 98.4 0.051 14.4 3.6 80482 79197 23.9
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 1.65 1.71 91.1 0.286 3.4 3 7258
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 2DUQ 1.65 20 75208 75208 3976 98.39 0.2 0.2 0.199 0.2028 0.228 0.2314 RANDOM 28
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] 0.66 1.48 0.26 1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.805 r_dihedral_angle_3_deg 13.752 r_dihedral_angle_4_deg 10.88 r_dihedral_angle_1_deg 6.304 r_scangle_it 2.958 r_scbond_it 1.931 r_mcangle_it 1.385 r_angle_refined_deg 1.318 r_mcbond_it 0.888 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.805 r_dihedral_angle_3_deg 13.752 r_dihedral_angle_4_deg 10.88 r_dihedral_angle_1_deg 6.304 r_scangle_it 2.958 r_scbond_it 1.931 r_mcangle_it 1.385 r_angle_refined_deg 1.318 r_mcbond_it 0.888 r_nbtor_refined 0.307 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.179 r_xyhbond_nbd_refined 0.111 r_symmetry_hbond_refined 0.104 r_chiral_restr 0.09 r_metal_ion_refined 0.057 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 4050 Nucleic Acid Atoms Solvent Atoms 418 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing