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OUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI, WITH BOUND CALCIUM AND CYANOCOBALAMIN (VITAMIN B12) SUBSTRATE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NQF PDB ENTRY 1NQF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.6 293 PEG 3350, MAGNESIUM ACETATE, BIS-TRIS, N-OCTYL TETRAOXYETHYLENE, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.28 62.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.687 α = 90 b = 81.687 β = 90 c = 225.814 γ = 120
Symmetry Space Group P 31 2 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 2002-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.6037 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.1 20 99.9 0.07 28.2 6.3 30657 30643 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.21 99.6 0.115 5.2 6.31 193476
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT + SAD THROUGHOUT PDB ENTRY 1NQF 3.1 20 15703 15679 837 99.85 0.2259 0.2238 0.2299 0.2646 RANDOM 23.448
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] -0.91 -0.46 -0.91 1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 25.749 r_dihedral_angle_1_deg 12.159 r_scangle_it 8.661 r_scbond_it 5.949 r_mcangle_it 3.632 r_angle_refined_deg 3.097 r_mcbond_it 2.238 r_angle_other_deg 1.259 r_chiral_restr 0.409 r_nbd_refined 0.391
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 25.749 r_dihedral_angle_1_deg 12.159 r_scangle_it 8.661 r_scbond_it 5.949 r_mcangle_it 3.632 r_angle_refined_deg 3.097 r_mcbond_it 2.238 r_angle_other_deg 1.259 r_chiral_restr 0.409 r_nbd_refined 0.391 r_nbd_other 0.366 r_symmetry_vdw_other 0.332 r_symmetry_vdw_refined 0.296 r_symmetry_hbond_refined 0.275 r_xyhbond_nbd_other 0.236 r_xyhbond_nbd_refined 0.234 r_nbtor_other 0.068 r_gen_planes_refined 0.043 r_bond_refined_d 0.032 r_gen_planes_other 0.018 r_bond_other_d 0.001 r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4630 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 223
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling AMoRE phasing SHARP phasing REFMAC refinement HKL-2000 data reduction