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Crystal structure of human ADP-ribosylation factor-like 6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZD9 pdb entries 1zd9, 2H16 experimental model PDB 2H16 pdb entries 1zd9, 2H16
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 2M ammonium sulfate, 0.2M sodium chloride, 0.1M sodium cacodylate, pH 5.5, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.1 60.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.058 α = 90 b = 134.885 β = 90 c = 63.884 γ = 90
Symmetry Space Group P 21 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 IMAGE PLATE RIGAKU RAXIS 2006-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.5418
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 30 97.9 0.043 17.6 5.3 46561
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) 2 2.07 96.2 0.599 5.2
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-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 1zd9, 2H16 2 30 46505 1777 97.889 0.207 0.20749 0.2059 0.2108 0.2453 0.2488 thin shells 34.198
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] -1.23 2.829 -1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.772 r_dihedral_angle_4_deg 21.932 r_dihedral_angle_3_deg 12.527 r_dihedral_angle_1_deg 6.112 r_mcangle_it 3.699 r_scangle_it 3.102 r_mcbond_it 2.54 r_scbond_it 2.274 r_angle_refined_deg 1.393 r_angle_other_deg 1.039
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.772 r_dihedral_angle_4_deg 21.932 r_dihedral_angle_3_deg 12.527 r_dihedral_angle_1_deg 6.112 r_mcangle_it 3.699 r_scangle_it 3.102 r_mcbond_it 2.54 r_scbond_it 2.274 r_angle_refined_deg 1.393 r_angle_other_deg 1.039 r_mcbond_other 0.59 r_symmetry_vdw_other 0.242 r_symmetry_vdw_refined 0.199 r_nbd_refined 0.196 r_nbd_other 0.191 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.128 r_metal_ion_refined 0.092 r_chiral_restr 0.08 r_nbtor_other 0.079 r_symmetry_hbond_refined 0.067 r_bond_refined_d 0.018 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3918 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 108
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction