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Human Vps33A in complex with a fragment of human Vps16
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BX8 PDB ENTRY 4BX8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 CRYSTALS WERE GROWN IN SITTING DROPS AT 20C. VPS33A:VPS16 COMPLEX (200 NL; A280 = 7.13, APPROX. 8.7 MG/ML) WAS MIXED 1:1 WITH RESERVOIR SOLUTION AND EQUILIBRATED AGAINST 80 UL RESERVOIRS CONTAINING 4% TACSIMATE PH 6.0, 12% PEG 3350 (HAMPTON RESEARCH). CRYSTALS WERE CRYOPROTECTED BY BRIEF IMMERSION IN RESERVOIR SOLUTION SUPPLEMENTED WITH 30% ETHYLENE GLYCOL AND CRYO-COOLED BY PLUNGING INTO LIQUID NITROGEN.
Crystal Properties Matthews coefficient Solvent content 3.64 66.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.41 α = 90 b = 128.41 β = 90 c = 263.36 γ = 90
Symmetry Space Group P 43 21 2
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 2M TOROIDAL 2012-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 2.6 87.8 100 0.11 16.8 15.2 68560 -3 76.138
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 2.6 2.72 100 1.31 2.1 14
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 ENTRY 4BX8 2.6 85.84 65003 3465 99.98 0.17762 0.17594 0.1804 0.21024 0.2098 RANDOM 70.508
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] -0.75 -0.75 1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.529 r_dihedral_angle_4_deg 19.91 r_dihedral_angle_3_deg 16.432 r_dihedral_angle_1_deg 6.239 r_angle_refined_deg 1.756 r_angle_other_deg 1.092 r_chiral_restr 0.094 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.529 r_dihedral_angle_4_deg 19.91 r_dihedral_angle_3_deg 16.432 r_dihedral_angle_1_deg 6.239 r_angle_refined_deg 1.756 r_angle_other_deg 1.092 r_chiral_restr 0.094 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.005 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9973 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing