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X-ray structure of NifS-like protein from Rickettsia africae ESF-5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P3W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 Microlytics MCSG1 screen a12: 200mM CaCl2, 20% PEG 4000, 100mM Tris, RiafA.00081.a.B1.PW36482 at 20mg/ml , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.27 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.02 α = 90 b = 91.02 β = 93.72 c = 72.62 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 CCD ADSC QUANTUM 315r 2012-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.2 50 99.9 0.118 0.118 12.4 4.6 37653 37634
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 100 0.499 3.05 3.05 4.65 2725
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1p3w 2.2 48.29 37653 37613 1878 99.95 0.1644 0.1644 0.1623 0.2047 0.1831 RANDOM 22.2603
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] 0.16 -0.76 0.11 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.809 r_dihedral_angle_4_deg 20.477 r_dihedral_angle_3_deg 12.616 r_dihedral_angle_1_deg 5.464 r_mcangle_it 1.369 r_angle_refined_deg 1.35 r_angle_other_deg 0.976 r_mcbond_it 0.8 r_mcbond_other 0.799 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.809 r_dihedral_angle_4_deg 20.477 r_dihedral_angle_3_deg 12.616 r_dihedral_angle_1_deg 5.464 r_mcangle_it 1.369 r_angle_refined_deg 1.35 r_angle_other_deg 0.976 r_mcbond_it 0.8 r_mcbond_other 0.799 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5470 Nucleic Acid Atoms Solvent Atoms 407 Heterogen Atoms 9
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction BOS data collection XDS data reduction XSCALE data scaling