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Structure of the GGA1-appendage in complex with the p56 binding peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NA8 PDB ID 1NA8 chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 288 100 mM sodium citrate, 100 mM MgCl2 and 35% PEG 400, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.31 46.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.414 α = 90 b = 61.414 β = 90 c = 145.008 γ = 120
Symmetry Space Group P 31 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 2003-01-05 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 2.5 30 99.9 0.081 16.5 4.9 11523 11512 3.1 55.4
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) 2.5 2.64 99.9 0.478 3.1 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 ID 1NA8 chain A 2.5 30 3.1 1.55 10957 553 99.84 0.21569 0.21338 0.2094 0.26203 0.2582 RANDOM 42.167
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] -0.2 -0.1 -0.2 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.587 r_scangle_it 4.19 r_scbond_it 2.37 r_mcangle_it 1.919 r_angle_refined_deg 1.815 r_mcbond_it 1.022 r_angle_other_deg 0.941 r_symmetry_vdw_other 0.276 r_nbd_other 0.238 r_xyhbond_nbd_refined 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.587 r_scangle_it 4.19 r_scbond_it 2.37 r_mcangle_it 1.919 r_angle_refined_deg 1.815 r_mcbond_it 1.022 r_angle_other_deg 0.941 r_symmetry_vdw_other 0.276 r_nbd_other 0.238 r_xyhbond_nbd_refined 0.22 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.194 r_chiral_restr 0.096 r_nbtor_other 0.095 r_symmetry_hbond_refined 0.066 r_bond_refined_d 0.021 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_xyhbond_nbd_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 2380 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement CCP4 data scaling