☰ Navigation Tabs
1.9 Angstrom Crystal Structure of the Rat VAP-A MSP Homology Domain in Complex with the Rat ORP1 FFAT Motif
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z9L Found Se by molecular replacement w/ 1Z9L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 283 PEG 2000 MME, sodium thiocyanate, tris buffer, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.12 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.048 α = 90.01 b = 50.033 β = 90 c = 90.287 γ = 60.03
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 QUANTUM 4 2004-08-28 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 4 2004-08-28 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0331 ALS 8.2.1 2 SYNCHROTRON ALS BEAMLINE 8.2.1 0.9794 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 50 4 59859 59506 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 1.9 1.949 100
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT Found Se by molecular replacement w/ 1Z9L 1.9 14.65 53477 53477 6029 100 0.21941 0.21472 0.2284 0.26051 RANDOM 26.342
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] 1.01 -0.45 0.05 1 -0.02 -1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.45 r_dihedral_angle_3_deg 19.326 r_dihedral_angle_4_deg 19.094 r_dihedral_angle_1_deg 7.322 r_scangle_it 4.613 r_scbond_it 3.466 r_angle_refined_deg 2.492 r_mcangle_it 2.093 r_mcbond_it 1.786 r_angle_other_deg 1.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.45 r_dihedral_angle_3_deg 19.326 r_dihedral_angle_4_deg 19.094 r_dihedral_angle_1_deg 7.322 r_scangle_it 4.613 r_scbond_it 3.466 r_angle_refined_deg 2.492 r_mcangle_it 2.093 r_mcbond_it 1.786 r_angle_other_deg 1.135 r_mcbond_other 0.504 r_symmetry_vdw_other 0.305 r_xyhbond_nbd_refined 0.22 r_nbd_other 0.215 r_symmetry_vdw_refined 0.199 r_nbd_refined 0.192 r_nbtor_refined 0.192 r_symmetry_hbond_refined 0.183 r_chiral_restr 0.153 r_xyhbond_nbd_other 0.107 r_nbtor_other 0.102 r_bond_refined_d 0.031 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6144 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling CNS phasing