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Crystal structure of the GAP domain of SMAP1L (LOC64744) stromal membrane-associated protein 1-like
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CRR PDB entry 2CRR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 25% PEG-3350, 0.2M Ammonium acetate, 0.1M Bis-Tris, pH 6.5, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.1 40.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.812 α = 90.1 b = 38.513 β = 108.89 c = 47.386 γ = 105.13
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 2006-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.54180
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 1.85 20 94.1 0.052 14.3 3.9 17983
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) 1.85 1.92 90.5 0.381 3.9
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R PDB entry 2CRR 1.9 20 16648 998 94.334 0.195 0.1915 0.2457 0.236 thin shells 20.834
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] 0.336 -0.612 0.204 0.198 -0.296 -0.722
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.238 r_dihedral_angle_4_deg 16.666 r_dihedral_angle_3_deg 12.665 r_dihedral_angle_1_deg 6.342 r_scangle_it 3.527 r_mcangle_it 3.206 r_mcbond_it 2.717 r_scbond_it 2.471 r_angle_refined_deg 1.358 r_angle_other_deg 0.956
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.238 r_dihedral_angle_4_deg 16.666 r_dihedral_angle_3_deg 12.665 r_dihedral_angle_1_deg 6.342 r_scangle_it 3.527 r_mcangle_it 3.206 r_mcbond_it 2.717 r_scbond_it 2.471 r_angle_refined_deg 1.358 r_angle_other_deg 0.956 r_mcbond_other 0.797 r_symmetry_vdw_other 0.208 r_nbd_refined 0.198 r_nbd_other 0.189 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.137 r_symmetry_vdw_refined 0.131 r_symmetry_hbond_refined 0.098 r_chiral_restr 0.085 r_nbtor_other 0.084 r_bond_refined_d 0.017 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 1941 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 11
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction DM phasing