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Complex of human VARP-ANKRD1 with Rab32-GppCp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YHN PDB ENTRIES 1YHN AND 4B93 experimental model PDB 4B93 PDB ENTRIES 1YHN AND 4B93
Crystallization Crystal Properties Matthews coefficient Solvent content 2.82 56.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.445 α = 90 b = 144.445 β = 90 c = 135.68 γ = 120
Symmetry Space Group P 32 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 PIXEL DECTRIS PILATUS 6M 2012-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 2.8 72.22 98.8 0.24 8.8 7.4 40077
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 2.8 2.91 94.1 1.5 0.9 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 (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 ENTRIES 1YHN AND 4B93 2.8 125.09 38004 2011 98.33 0.19466 0.19205 0.2006 0.24565 0.2465 RANDOM 74.856
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] 1.4 0.7 1.4 -4.53
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 11.745 r_long_range_B_refined 11.743 r_scangle_other 8.749 r_mcangle_it 8.083 r_mcangle_other 8.083 r_scbond_it 5.522 r_scbond_other 5.522 r_mcbond_it 5.212 r_mcbond_other 5.2 r_angle_refined_deg 1.539
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 11.745 r_long_range_B_refined 11.743 r_scangle_other 8.749 r_mcangle_it 8.083 r_mcangle_other 8.083 r_scbond_it 5.522 r_scbond_other 5.522 r_mcbond_it 5.212 r_mcbond_other 5.2 r_angle_refined_deg 1.539 r_angle_other_deg 1.076 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.004 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg 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 8052 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing