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Crystal structure of human synaptic vesicle membrane protein VAT-1 homolog-like protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YB5 PDB ENTRY 1YB5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.20 M NABR, 0.1 M BISTRISPROPANE PH 6.5, 20.0% PEG 3350, 10.0% ETHYLENE GLYCOL.
Crystal Properties Matthews coefficient Solvent content 2.26 45.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.509 α = 90 b = 62.104 β = 106.98 c = 83.795 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 ADSC CCD 2011-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 2.1 19.76 99.8 0.08 12.6 4.7 40044 2.3 39.3
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 2.1 2.21 99.9 0.64 2.3 4.2
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 MIRAS THROUGHOUT PDB ENTRY 1YB5 2.1 19.59 38011 2009 99.76 0.18702 0.1848 0.1875 0.22956 0.2275 RANDOM 43.655
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] -1.1 -3.25 -0.12 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.221 r_dihedral_angle_4_deg 18.261 r_dihedral_angle_3_deg 14.361 r_dihedral_angle_1_deg 6.307 r_angle_refined_deg 1.517 r_angle_other_deg 1.152 r_chiral_restr 0.091 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.221 r_dihedral_angle_4_deg 18.261 r_dihedral_angle_3_deg 14.361 r_dihedral_angle_1_deg 6.307 r_angle_refined_deg 1.517 r_angle_other_deg 1.152 r_chiral_restr 0.091 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 4681 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling SHARP phasing