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VCP-interacting membrane protein (VIMP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q2F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 288 0.1 M MES, pH 6.0, 20 % 2-propanol, 20 % PEG MME 2000
Crystal Properties Matthews coefficient Solvent content 1.9 35.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.729 α = 90 b = 17.973 β = 95.58 c = 33.993 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 100 CCD RAYONIX MX300-HS 2011-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1 APS 21-ID-D
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 2.2 60.58 92 11 3 3854
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 2.2 2.28 0.286
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 MOLECULAR REPLACEMENT THROUGHOUT 2Q2F 2.2 60.58 3681 173 97.15 0.1885 0.18576 0.1948 0.24434 0.2479 RANDOM 48.188
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] 0.04 3.07 -1.55 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.193 r_dihedral_angle_4_deg 19.862 r_dihedral_angle_3_deg 18.532 r_long_range_B_other 8.092 r_long_range_B_refined 7.991 r_scangle_other 6.245 r_dihedral_angle_1_deg 5.535 r_scbond_it 3.776 r_scbond_other 3.771 r_mcangle_it 3.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.193 r_dihedral_angle_4_deg 19.862 r_dihedral_angle_3_deg 18.532 r_long_range_B_other 8.092 r_long_range_B_refined 7.991 r_scangle_other 6.245 r_dihedral_angle_1_deg 5.535 r_scbond_it 3.776 r_scbond_other 3.771 r_mcangle_it 3.221 r_mcangle_other 3.221 r_mcbond_it 2.114 r_mcbond_other 2.036 r_angle_refined_deg 1.943 r_angle_other_deg 1.059 r_chiral_restr 0.127 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 631 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing