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Crystal structure of a membrane protein from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AZO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 PEG 4000, sodium acetate, sodium formate
Crystal Properties Matthews coefficient Solvent content 4.55 72.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 257.515 α = 90 b = 257.515 β = 90 c = 81.825 γ = 90
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 RAYONIX MX300HE 2015-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
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 1.69 50 99.5 22.9 3.6 297648
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 (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 5AZO 1.69 50 282614 15033 99.4 0.16109 0.16008 0.1728 0.17974 0.1909 RANDOM 26.502
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] -0.05 -0.05 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.095 r_dihedral_angle_4_deg 19.251 r_dihedral_angle_3_deg 12.465 r_long_range_B_other 9.01 r_long_range_B_refined 9.009 r_dihedral_angle_1_deg 5.04 r_scangle_other 4.644 r_scbond_it 3.08 r_scbond_other 3.079 r_mcangle_it 2.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.095 r_dihedral_angle_4_deg 19.251 r_dihedral_angle_3_deg 12.465 r_long_range_B_other 9.01 r_long_range_B_refined 9.009 r_dihedral_angle_1_deg 5.04 r_scangle_other 4.644 r_scbond_it 3.08 r_scbond_other 3.079 r_mcangle_it 2.155 r_mcangle_other 2.155 r_angle_refined_deg 1.973 r_mcbond_it 1.523 r_mcbond_other 1.494 r_angle_other_deg 1.097 r_chiral_restr 0.125 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10290 Nucleic Acid Atoms Solvent Atoms 1885 Heterogen Atoms 379
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing