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Structure of a domain from the type IV pilus biogenesis lipoprotein PilP, from Pseudomonas aeruginosa PA01
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y4Y PDB ENTRY 2Y4Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1M HEPES PH 7.5, 8% (V/V) ETHYLENE GLYCOL, 20% (W/V) PEG 10,000
Crystal Properties Matthews coefficient Solvent content 2.1 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.24 α = 90 b = 87.79 β = 103.77 c = 42.21 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE RIGAKU R-AXIS IV MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 1.7 30 86.7 0.06 9.7 2.8 16259 2.4
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 1.7 1.79 85.8 0.38 2.4 2.9
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 PDB ENTRY 2Y4Y 1.7 30 15372 842 85.9 0.233 0.23 0.2268 0.282 0.2797 RANDOM 16.23
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] -0.2 -0.35 -0.31 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.249 r_dihedral_angle_4_deg 18.299 r_dihedral_angle_3_deg 16.171 r_dihedral_angle_1_deg 7.959 r_scangle_it 6.907 r_scbond_it 5.107 r_mcangle_it 2.833 r_rigid_bond_restr 2.561 r_angle_refined_deg 2.321 r_mcbond_it 1.954
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.249 r_dihedral_angle_4_deg 18.299 r_dihedral_angle_3_deg 16.171 r_dihedral_angle_1_deg 7.959 r_scangle_it 6.907 r_scbond_it 5.107 r_mcangle_it 2.833 r_rigid_bond_restr 2.561 r_angle_refined_deg 2.321 r_mcbond_it 1.954 r_chiral_restr 0.145 r_bond_refined_d 0.028 r_gen_planes_refined 0.01 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1344 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing