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High resolution Crystal structure of Transmembrane domain of M2 protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C9J Amantandine-bound M2TM; G34A mutant
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 298 Protein solution: 0.8mM protein, 32mM n-octyl-beta-D-glucopyranoside and 5%v/v xylitol.
Reservoir solution: 50mM Tris-Hcl, 500mM MgCl2, 21% PEG 350 MME, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.67 53.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.753 α = 90 b = 56.557 β = 103.53 c = 56.009 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 315 2001-10-01 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.97853 NSLS X25
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 50 94.9 0.062 22.4 3.4 15355 14567 1 37.1
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 2 2.05 75.1 0.305 1.9 2 777
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 (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 Amantandine-bound M2TM; G34A mutant 2.05 20 14047 747 99.32 0.244 0.22158 0.21908 0.2209 0.26871 0.2765 RANDOM 31.117
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] -0.12 -0.04 2.17 -2.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.195 r_dihedral_angle_4_deg 19.918 r_dihedral_angle_3_deg 13.966 r_dihedral_angle_1_deg 4.424 r_scangle_it 2.289 r_scbond_it 1.662 r_angle_refined_deg 1.348 r_mcangle_it 1.147 r_mcbond_it 0.887 r_xyhbond_nbd_refined 0.499
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.195 r_dihedral_angle_4_deg 19.918 r_dihedral_angle_3_deg 13.966 r_dihedral_angle_1_deg 4.424 r_scangle_it 2.289 r_scbond_it 1.662 r_angle_refined_deg 1.348 r_mcangle_it 1.147 r_mcbond_it 0.887 r_xyhbond_nbd_refined 0.499 r_nbtor_refined 0.299 r_symmetry_hbond_refined 0.202 r_symmetry_vdw_refined 0.2 r_nbd_refined 0.188 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 1544 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 164
Software Software Software Name Purpose CBASS data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling