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Crystal structure of RavD (residues 1-200) from Legionella pneumophila (strain Corby)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NJD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 289 0.1 M MMT (Malic Acid, MES and TRIS (1:2:2 Molar Ratio), pH 4.5 adjusted with HCl), 0.2 M ammonium chloride, 15% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.37 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.335 α = 90 b = 142.335 β = 90 c = 55.215 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 PILATUS 6M 2018-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97930 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.15 50.01 100 0.107 0.114 0.039 5 8.4 22916
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 2.15 2.19 99.8 0.803 0.863 0.313 0.835 7.2
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 6NJD 2.15 50.01 21459 1218 99.97 0.197 0.1949 0.1973 0.2321 0.2317 RANDOM 53.159
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] -1.13 -0.57 -1.13 3.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.361 r_dihedral_angle_4_deg 17.407 r_dihedral_angle_3_deg 14.672 r_dihedral_angle_1_deg 6.518 r_angle_refined_deg 1.296 r_angle_other_deg 0.896 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.361 r_dihedral_angle_4_deg 17.407 r_dihedral_angle_3_deg 14.672 r_dihedral_angle_1_deg 6.518 r_angle_refined_deg 1.296 r_angle_other_deg 0.896 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2707 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHENIX phasing