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Crystal structure of the GRASP55 GRASP Domain with a phosphomimetic mutation (S189D)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RLE PDB ENTRY 3RLE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 277 0.2M ammonium acetate, 0.1M Tris pH 9.0, 0.1M immidazole, 30% PEG 4000, 10% PEG 20,000, 10% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.46 49.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.857 α = 90 b = 82.547 β = 90 c = 84.059 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 RIGAKU SATURN 944 2010-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54148
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.9 58.9 98 0.087 22.2 5.9 35319 34613 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 99.9 0.646 2.74 5.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) 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 ENTRY 3RLE 1.901 58.9 2 35319 33386 1747 97.04 0.21164 0.21164 0.20862 0.2146 0.27052 0.2716 RANDOM 37.712
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] 1.08 -0.04 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.123 r_dihedral_angle_4_deg 18.332 r_dihedral_angle_3_deg 16.467 r_dihedral_angle_1_deg 6.578 r_scangle_it 5.128 r_scbond_it 3.187 r_mcangle_it 2.045 r_angle_refined_deg 1.927 r_mcbond_it 1.169 r_chiral_restr 0.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.123 r_dihedral_angle_4_deg 18.332 r_dihedral_angle_3_deg 16.467 r_dihedral_angle_1_deg 6.578 r_scangle_it 5.128 r_scbond_it 3.187 r_mcangle_it 2.045 r_angle_refined_deg 1.927 r_mcbond_it 1.169 r_chiral_restr 0.141 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3161 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 1
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling