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PaxB from Photorhabdus luminescens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Semet derivative of PaxB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.2 M MgCl2; 0.1 M Bis-Tris, 25% PEG 3350; 0.2M NaSCN
Crystal Properties Matthews coefficient Solvent content 2.93 58.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.59 α = 90 b = 70.18 β = 108.41 c = 136.89 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 PIXEL DECTRIS EIGER X 16M 2015-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 2.8 30 95.3 0.069 0.997 9.7 2.9 44675
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 94.7 0.515 0.729 1.8
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 Semet derivative of PaxB 2.8 15 42429 2234 95.37 0.24205 0.2405 0.2494 0.26835 0.2803 RANDOM 85.879
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] -3.67 0.04 -2.37 4.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.621 r_dihedral_angle_3_deg 14.744 r_dihedral_angle_4_deg 10.761 r_dihedral_angle_1_deg 3.992 r_long_range_B_refined 3.601 r_long_range_B_other 3.554 r_mcangle_it 1.527 r_mcangle_other 1.527 r_scangle_other 1.162 r_mcbond_it 0.834
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.621 r_dihedral_angle_3_deg 14.744 r_dihedral_angle_4_deg 10.761 r_dihedral_angle_1_deg 3.992 r_long_range_B_refined 3.601 r_long_range_B_other 3.554 r_mcangle_it 1.527 r_mcangle_other 1.527 r_scangle_other 1.162 r_mcbond_it 0.834 r_mcbond_other 0.834 r_angle_refined_deg 0.696 r_angle_other_deg 0.646 r_scbond_it 0.607 r_scbond_other 0.607 r_chiral_restr 0.041 r_bond_refined_d 0.004 r_gen_planes_refined 0.002 r_bond_other_d 0.001 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 10648 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing