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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 6 293 PEG 4000, sodium acetate, sodium formate
Crystal Properties Matthews coefficient Solvent content 3.29 62.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.329 α = 90 b = 92.388 β = 90 c = 252.765 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 RAYONIX MX300HE 2015-04-12 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 3.1 50 97.2 20.9 4.5 36834
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 1WP1 3.1 50 34702 1807 97.17 0.27051 0.26861 0.279 0.30744 0.3163 RANDOM 113.175
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] 10.78 -5.69 -5.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.074 r_dihedral_angle_3_deg 17.867 r_dihedral_angle_4_deg 16.218 r_dihedral_angle_1_deg 5.479 r_long_range_B_refined 4.508 r_long_range_B_other 4.508 r_mcangle_it 2.654 r_mcangle_other 2.654 r_scangle_other 2.534 r_mcbond_it 1.522
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.074 r_dihedral_angle_3_deg 17.867 r_dihedral_angle_4_deg 16.218 r_dihedral_angle_1_deg 5.479 r_long_range_B_refined 4.508 r_long_range_B_other 4.508 r_mcangle_it 2.654 r_mcangle_other 2.654 r_scangle_other 2.534 r_mcbond_it 1.522 r_mcbond_other 1.521 r_scbond_it 1.411 r_scbond_other 1.411 r_angle_refined_deg 1.124 r_angle_other_deg 0.908 r_chiral_restr 0.057 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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 10096 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing