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Crystal structure of ADP-ribosylation factor binding protein GGA1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GYU PDB ID 1GYU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 289 sodium citrate, ammonium sulphate, pH 5.6,
VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.52 50.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.426 α = 90 b = 65.426 β = 90 c = 142.725 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 IMAGE PLATE MARRESEARCH 2001-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 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 2.3 57 99 0.053 23.7 5.6 16193 5.9 -3 45
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 2.3 2.36 99 0.306 5.9 5.7
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 ID 1GYU 2.3 15 15310 813 98.93 0.21869 0.21869 0.21571 0.221 0.27923 0.2825 RANDOM 23.119
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] 1.92 0.96 1.92 -2.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.167 r_scangle_it 3.992 r_dihedral_angle_1_deg 3.689 r_scbond_it 2.31 r_angle_refined_deg 1.718 r_mcangle_it 1.483 r_mcbond_it 0.803 r_angle_other_deg 0.802 r_symmetry_hbond_refined 0.563 r_symmetry_vdw_refined 0.269
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.167 r_scangle_it 3.992 r_dihedral_angle_1_deg 3.689 r_scbond_it 2.31 r_angle_refined_deg 1.718 r_mcangle_it 1.483 r_mcbond_it 0.803 r_angle_other_deg 0.802 r_symmetry_hbond_refined 0.563 r_symmetry_vdw_refined 0.269 r_symmetry_vdw_other 0.264 r_nbd_refined 0.239 r_nbd_other 0.236 r_xyhbond_nbd_refined 0.169 r_xyhbond_nbd_other 0.106 r_chiral_restr 0.091 r_bond_refined_d 0.019 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_nbtor_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2327 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement CNS refinement CCP4 data scaling