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VHS Domain of human GGA1 complexed with cation-independent M6PR C-terminal Peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JWF PDB ENTRY 1JWF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 PEG 3350, ammonium iodide, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.55 51.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.146 α = 90 b = 65.77 β = 90 c = 101.426 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2001-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 99.6 24632 24632
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.11 99.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1JWF 2 30 24632 24632 1292 99.67 0.22796 0.22796 0.2263 0.26115 RANDOM 39.099
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] -0.89 2.78 -1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.756 r_scangle_it 3.976 r_dihedral_angle_1_deg 2.975 r_scbond_it 2.326 r_mcangle_it 1.54 r_angle_refined_deg 1.286 r_mcbond_it 0.815 r_nbd_refined 0.245 r_xyhbond_nbd_refined 0.183 r_symmetry_vdw_refined 0.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.756 r_scangle_it 3.976 r_dihedral_angle_1_deg 2.975 r_scbond_it 2.326 r_mcangle_it 1.54 r_angle_refined_deg 1.286 r_mcbond_it 0.815 r_nbd_refined 0.245 r_xyhbond_nbd_refined 0.183 r_symmetry_vdw_refined 0.178 r_symmetry_hbond_refined 0.173 r_chiral_restr 0.093 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_symmetry_vdw_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 2355 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 6
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement CCP4 data scaling