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High resolution crystal structure of transmembrane domain of M2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BKD 3BKD, chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 Protein solution: 0.8mM M2TM (25-46) peptide (as monomer),28mM Octyl-beta-D-Glucopyranosie and 5% xylitol. Reservoir solution: 95% [100mM sodium citrate pH 5.6, 150mM tri-sodium citrate, 15% v/v isopropanol] and 5% [0.2M MgCl2 6H20, 0.1M Tris-Hcl pH 8.5, 30% w/v PEG 4000], VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.38 48.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.665 α = 90 b = 79.091 β = 90 c = 48.559 γ = 90
Symmetry Space Group C 2 2 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 210 2008-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.91910 NSLS X6A
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 1.65 48.56 99.5 0.07 19.4 6.6 11567 11509 1 1 15.278
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 1.65 1.74 96.6 0.447 2.7 4.5 1599
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3BKD, chain A 1.65 31.53 10998 10998 554 100 0.207 0.19664 0.19621 0.2066 0.20529 0.2173 RANDOM 15.431
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] -0.16 0.14 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 53.922 r_dihedral_angle_4_deg 19.336 r_dihedral_angle_3_deg 11.004 r_dihedral_angle_1_deg 2.858 r_scangle_it 2.043 r_scbond_it 1.229 r_angle_refined_deg 0.866 r_mcangle_it 0.806 r_mcbond_it 0.455 r_chiral_restr 0.054
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 53.922 r_dihedral_angle_4_deg 19.336 r_dihedral_angle_3_deg 11.004 r_dihedral_angle_1_deg 2.858 r_scangle_it 2.043 r_scbond_it 1.229 r_angle_refined_deg 0.866 r_mcangle_it 0.806 r_mcbond_it 0.455 r_chiral_restr 0.054 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 696 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 67
Software Software Software Name Purpose CBASS data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling