☰ Navigation Tabs
SEC7 DOMAIN OF THE ARF EXCHANGE FACTOR ARNO WITH BREFELDIN A-SENSITIZING MUTATIONS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PBV PDB ENTRY 1PBV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 289 20% PEG 3350, 190mM Sodium Formate, 100mM Hepes, 18mM MnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.24 45.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.429 α = 90 b = 95.775 β = 101.67 c = 33.665 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 M SINGLE WAVELENGTH 2 1 x-ray 100 M 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.979 ESRF BM30A 2 SYNCHROTRON ESRF BEAMLINE ID14-3 0.933 ESRF ID14-3
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 1.7 33 0.066 18 4.5 21082 17.61
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 1.7 1.75 65.5 0.122 5 1.76
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1PBV 1.7 32.97 21082 19998 1083 93.12 0.19414 0.19209 0.2035 0.23136 0.2402 RANDOM 15.946
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] -0.19 0.59 -0.59 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.332 r_scangle_it 5.98 r_scbond_it 3.821 r_mcangle_it 2.245 r_angle_refined_deg 1.942 r_mcbond_it 1.306 r_angle_other_deg 1.091 r_symmetry_vdw_refined 0.365 r_symmetry_vdw_other 0.328 r_nbd_other 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.332 r_scangle_it 5.98 r_scbond_it 3.821 r_mcangle_it 2.245 r_angle_refined_deg 1.942 r_mcbond_it 1.306 r_angle_other_deg 1.091 r_symmetry_vdw_refined 0.365 r_symmetry_vdw_other 0.328 r_nbd_other 0.24 r_nbd_refined 0.235 r_xyhbond_nbd_refined 0.164 r_symmetry_hbond_refined 0.163 r_chiral_restr 0.11 r_nbtor_other 0.093 r_bond_refined_d 0.025 r_gen_planes_other 0.023 r_gen_planes_refined 0.017 r_bond_other_d 0.003 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_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 1593 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling AMoRE phasing