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Structure of Nal1 protein , SPIKE allele from japonica rice, construct 46-458
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8PME
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.1M MES
10% PEG 5000 MME
10% 1-propanol
Crystal Properties Matthews coefficient Solvent content 2.63 53.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 175.428 α = 90 b = 193.36 β = 90 c = 84.037 γ = 90
Symmetry Space Group P 21 21 2
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 2020-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.978690 SSRF BL19U1
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 2.948 129.924 90.4 0.236 0.245 0.067 0.997 11 13.3 47426 71.73
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 2.948 3.19 52.1 1.957 2.035 0.553 0.644 1.5 13.5
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 2.95 87.71 1.36 47343 2269 77.38 0.2074 0.2051 0.2051 0.252 0.2522 70.19
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 13.8944 f_angle_d 1.1377 f_chiral_restr 0.0565 f_bond_d 0.0061 f_plane_restr 0.0058
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18585 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 192
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing