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VIP3B (VIP3B_2160) adapted for crystallization
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other truncated protein (structure to be published)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 25% PEG 1500, 100 mM Bis-Tris Propane pH 9.0, 100 mM NaCl.
Crystal Properties Matthews coefficient Solvent content 3.39 63.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.488 α = 96.13 b = 106.542 β = 70.93 c = 117.728 γ = 69.52
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 MARMOSAIC 325 mm CCD 2014-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.189 49.892 98.7 0.105 0.117 0.064 15.2 3.9 72704
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.189 3.26 98.9 0.95 0.95 0.668 0.388 3.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE truncated protein (structure to be published) 3.189 49.892 72704 3538 98.273 0.22 0.218 0.2151 0.2586 0.2545 107.401
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] 1.143 -2.691 -0.342 -0.801 -1.076 -0.977
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.13 r_dihedral_angle_4_deg 18.801 r_dihedral_angle_3_deg 18.598 r_lrange_it 16.959 r_lrange_other 16.959 r_scangle_it 12.647 r_scangle_other 12.645 r_mcangle_it 12.251 r_mcangle_other 12.251 r_scbond_it 8.033
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.13 r_dihedral_angle_4_deg 18.801 r_dihedral_angle_3_deg 18.598 r_lrange_it 16.959 r_lrange_other 16.959 r_scangle_it 12.647 r_scangle_other 12.645 r_mcangle_it 12.251 r_mcangle_other 12.251 r_scbond_it 8.033 r_scbond_other 8.031 r_mcbond_it 8.025 r_mcbond_other 8.025 r_dihedral_angle_1_deg 6.97 r_angle_refined_deg 1.571 r_angle_other_deg 1.514 r_nbd_other 0.396 r_symmetry_nbd_refined 0.304 r_symmetry_nbd_other 0.224 r_nbd_refined 0.219 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.136 r_symmetry_xyhbond_nbd_refined 0.124 r_ncsr_local_group_3 0.114 r_ncsr_local_group_5 0.11 r_ncsr_local_group_2 0.105 r_ncsr_local_group_4 0.105 r_ncsr_local_group_6 0.098 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.089 r_symmetry_xyhbond_nbd_other 0.08 r_ncsr_local_group_1 0.079 r_ext_dist_refined_d 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23683 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing