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Crystal structure of the holo form of the hemophore HasA from Pseudomonas protegens Pf-5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model SwissModel
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 100mM Sodium acetate/acetic acid (pH 4.5), 2.5M NaCl, 0.2M Lithium sulfate
Crystal Properties Matthews coefficient Solvent content 3.4 63.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.597 α = 90 b = 99.597 β = 90 c = 90.473 γ = 120
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 4M 2019-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.000 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.9 45.24 100 0.317 0.324 0.071 0.998 11.7 20.8 40219
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 100 4.823 4.936 1.047 0.584 21.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.9 20 38157 1984 99.86 0.16 0.1583 0.1679 0.1928 0.1989 RANDOM 28.239
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] -0.12 -0.06 -0.12 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.659 r_dihedral_angle_4_deg 16.786 r_dihedral_angle_3_deg 11.881 r_dihedral_angle_1_deg 7.571 r_angle_refined_deg 1.235 r_angle_other_deg 0.989 r_chiral_restr 0.063 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.659 r_dihedral_angle_4_deg 16.786 r_dihedral_angle_3_deg 11.881 r_dihedral_angle_1_deg 7.571 r_angle_refined_deg 1.235 r_angle_other_deg 0.989 r_chiral_restr 0.063 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2646 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 120
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing