☰ Navigation Tabs
Crystal structure of homodimeric Alba from Oryza sativa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VM0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 0.2 M SODIUM CACODYLATE pH 7, 0.2 M SODIUM BROMIDE, 23% Peg 5K MME
Crystal Properties Matthews coefficient Solvent content 2.59 52.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.89 α = 90 b = 71.89 β = 90 c = 174.31 γ = 120
Symmetry Space Group P 61 2 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 CCD MARMOSAIC 225 mm CCD 2015-11-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.95372 ESRF BM14
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 2.6 35.94 100 0.101 0.111 0.045 0.998 14.4 6.1 8854 31.6
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 2.6 2.72 100 0.909 0.991 0.39 0.736 2 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1VM0 2.6 35.7 1.34 8798 430 99.97 0.2102 0.2077 0.2079 0.2597 0.2602 66.34
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 5.9656 f_angle_d 0.9517 f_chiral_restr 0.0547 f_bond_d 0.0085 f_plane_restr 0.0064
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1751 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing