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Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+-bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R1Z PDB ENTRY 1R1Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 15% PEG4000, 1.5M NaCl, 0.1M MES (pH6.5), VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.91 57.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.7 α = 90 b = 45.4 β = 131.5 c = 116.1 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 210 2005-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 97.8 0.059 14.6 3.7 62420 61028 23.8
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 97.1 0.385 3.1 3.8 5986
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 1R1Z 1.8 20 57775 57775 3080 97.8 0.206 0.206 0.205 0.2053 0.241 0.2398 RANDOM 25.14
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] 1.25 1.74 0.03 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.585 r_dihedral_angle_3_deg 13.692 r_dihedral_angle_4_deg 10.133 r_dihedral_angle_1_deg 6.537 r_scangle_it 3.103 r_scbond_it 2.021 r_mcangle_it 1.413 r_angle_refined_deg 1.328 r_mcbond_it 0.884 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.585 r_dihedral_angle_3_deg 13.692 r_dihedral_angle_4_deg 10.133 r_dihedral_angle_1_deg 6.537 r_scangle_it 3.103 r_scbond_it 2.021 r_mcangle_it 1.413 r_angle_refined_deg 1.328 r_mcbond_it 0.884 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.197 r_nbd_refined 0.195 r_xyhbond_nbd_refined 0.136 r_symmetry_hbond_refined 0.102 r_chiral_restr 0.098 r_metal_ion_refined 0.059 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3957 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing