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Crystal structure of the E. coli BamCD complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YH6 2YH6 AND 2YHC experimental model PDB 2YHC 2YH6 AND 2YHC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9.2 295 0.2 M K2HPO4 and 20% PEG3350, pH 9.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.86 67.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.78 α = 90 b = 133.38 β = 100.15 c = 144.992 γ = 90
Symmetry Space Group I 1 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 MERIDIONALLY-BENT FUSED SILICA MIRROR WITH PALLADIUM AND UNCOATED STRIPES VERTICALLY- FOCUSING AT 6.6:1 DEMAGNIFICATION 2009-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 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 2.9 97.5 99.6 0.112 14.6 7.2 30529 5
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 2.9 3 99.8 0.393 5.4 7.2
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2YH6 AND 2YHC 2.9 97.45 30529 28975 1538 99.5 0.181 0.177 0.1774 0.243 0.2404 RANDOM 36.95
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] 0.7 1.96 -1.51 1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.791 r_dihedral_angle_4_deg 18.408 r_dihedral_angle_3_deg 16.733 r_dihedral_angle_1_deg 6.045 r_scangle_it 4.923 r_scbond_it 2.906 r_mcangle_it 2.028 r_mcbond_it 1.054 r_angle_refined_deg 0.972 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.791 r_dihedral_angle_4_deg 18.408 r_dihedral_angle_3_deg 16.733 r_dihedral_angle_1_deg 6.045 r_scangle_it 4.923 r_scbond_it 2.906 r_mcangle_it 2.028 r_mcbond_it 1.054 r_angle_refined_deg 0.972 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 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 6298 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 32
Software Software Software Name Purpose CBASS data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling