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Crystal structure of the OprM channel in a non-symmetrical space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 Sodium citrate 1M, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.88 57.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.9 α = 90 b = 70.2 β = 90 c = 344.5 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 QUANTUM 210 2006-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.931 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 36.71 98.7 69761 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.54 94.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1WP1 2.4 35 2 65916 5058 100 0.23996 0.23583 0.2345 0.2932 0.2888 RANDOM 31.597
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.675 r_dihedral_angle_4_deg 15.6 r_dihedral_angle_3_deg 14.031 r_dihedral_angle_1_deg 4.349 r_scangle_it 1.238 r_angle_refined_deg 0.888 r_scbond_it 0.691 r_mcangle_it 0.505 r_nbtor_refined 0.287 r_mcbond_it 0.265
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.675 r_dihedral_angle_4_deg 15.6 r_dihedral_angle_3_deg 14.031 r_dihedral_angle_1_deg 4.349 r_scangle_it 1.238 r_angle_refined_deg 0.888 r_scbond_it 0.691 r_mcangle_it 0.505 r_nbtor_refined 0.287 r_mcbond_it 0.265 r_symmetry_vdw_refined 0.218 r_nbd_refined 0.162 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.054 r_symmetry_hbond_refined 0.043 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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 10470 Nucleic Acid Atoms Solvent Atoms 539 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement ADSC data collection XDS data reduction XDS data scaling PHASER phasing