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Crystal Structure of the FERM domain of Merlin, the Neurofibromatosis 2 Tumor Suppressor Protein.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GC6 PDB ENTRY 1GC6.PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 THE PROTEIN WAS CRYSTALLIZED USING HANGING-DROP VAPOR DIFFUSION WIHTH 56% AMMONIUM SULFATE, 2% DIOXANE, 100 MM CACODYLATE, PH 6.5. A 1:1 RATIO OF PROTEIN TO WELL SOLUTION WAS USED.
Crystal Properties Matthews coefficient Solvent content 2.5 51.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.018 α = 90 b = 89.328 β = 90 c = 96.764 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 CCD 2001-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9B NSLS X9B
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 1.8 25 95.5 0.065 16.8 3.5 68182
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 1.8 1.86 97.2 0.662 2.33 3.4
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-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 1GC6.PDB 1.8 25 66303 985 95.5 0.193 0.2026 0.227 0.2297 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.706 r_scbond_it 2.22 r_mcangle_it 1.51 r_angle_other_deg 1.39 r_mcbond_it 0.805 r_dihedral_angle_3_deg 0.759 r_symmetry_hbond_refined 0.346 r_symmetry_vdw_refined 0.251 r_symmetry_vdw_other 0.244 r_xyhbond_nbd_refined 0.239
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.706 r_scbond_it 2.22 r_mcangle_it 1.51 r_angle_other_deg 1.39 r_mcbond_it 0.805 r_dihedral_angle_3_deg 0.759 r_symmetry_hbond_refined 0.346 r_symmetry_vdw_refined 0.251 r_symmetry_vdw_other 0.244 r_xyhbond_nbd_refined 0.239 r_nbd_refined 0.225 r_nbd_other 0.209 r_chiral_restr 0.123 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_angle_refined_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4912 Nucleic Acid Atoms Solvent Atoms 861 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing