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Crystal structure of root lateral formation protein (RLF) b5-domain from Oryza sativa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LF5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 291 JCSG+ A6: 20% (w/v) PEG 1000, 100 mM phosphate-citrate pH 4.2, 200 mM lithium sulfate. Cryoprotectant: 80% crystallization solution and 20% (w/v) glycerol.
Crystal Properties Matthews coefficient Solvent content 2.32 46.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.951 α = 90 b = 26.138 β = 95.5 c = 82.873 γ = 90
Symmetry Space Group P 1 2 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 EIGER2 XE 9M 2018-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-ID
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 1.55 45.79 97.6 0.071 0.081 0.039 0.998 11 4.1 36463
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 1.55 1.58 98.1 0.666 0.766 0.371 0.763 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.55 41.246 1.02 36453 1819 97.66 0.1762 0.175 0.185 0.1997 0.2075
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.417 f_angle_d 0.961 f_chiral_restr 0.052 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1681 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 91
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing