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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 1WP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 MPD, sodium acetate
Crystal Properties Matthews coefficient Solvent content 3.26 62.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.501 α = 90 b = 76.501 β = 90 c = 191.833 γ = 120
Symmetry Space Group P 3 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 RAYONIX MX300HE 2014-12-17 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 2.7 50 100 17.1 10.9 18601
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1WP1 2.7 50 17736 865 99.86 0.23345 0.23154 0.27189 0.2548 RANDOM 49.44
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] 1.16 0.58 1.16 -3.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.932 r_dihedral_angle_4_deg 20.242 r_dihedral_angle_3_deg 16.3 r_dihedral_angle_1_deg 5.21 r_long_range_B_refined 4.312 r_long_range_B_other 4.312 r_scangle_other 3.019 r_mcangle_other 2.481 r_mcangle_it 2.48 r_scbond_it 1.772
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.932 r_dihedral_angle_4_deg 20.242 r_dihedral_angle_3_deg 16.3 r_dihedral_angle_1_deg 5.21 r_long_range_B_refined 4.312 r_long_range_B_other 4.312 r_scangle_other 3.019 r_mcangle_other 2.481 r_mcangle_it 2.48 r_scbond_it 1.772 r_scbond_other 1.772 r_mcbond_it 1.476 r_mcbond_other 1.472 r_angle_refined_deg 1.336 r_angle_other_deg 0.924 r_chiral_restr 0.067 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 3413 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing