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Crystal structure of yellow lupine LlPR-10.1A protein in ligand-free form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ICX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 18% PEG4000, 0.2 M sodium acetate, 0.1 M HEPES
Crystal Properties Matthews coefficient Solvent content 1.83 32.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.065 α = 90 b = 56.501 β = 90 c = 61.938 γ = 90
Symmetry Space Group P 21 21 21
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 2009-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.32 30 99.9 0.059 19.7 3.7 29618
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.32 1.37 99.7 2 3.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1icx 1.32 28.27 28503 1059 99.7 0.15296 0.15076 0.21152 0.2467 RANDOM 19.97
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] -1.84 1.47 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.031 r_sphericity_free 33.557 r_sphericity_bonded 15.795 r_dihedral_angle_3_deg 12.599 r_rigid_bond_restr 7.261 r_dihedral_angle_1_deg 7.109 r_angle_refined_deg 1.818 r_angle_other_deg 0.961 r_dihedral_angle_4_deg 0.785 r_chiral_restr 0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.031 r_sphericity_free 33.557 r_sphericity_bonded 15.795 r_dihedral_angle_3_deg 12.599 r_rigid_bond_restr 7.261 r_dihedral_angle_1_deg 7.109 r_angle_refined_deg 1.818 r_angle_other_deg 0.961 r_dihedral_angle_4_deg 0.785 r_chiral_restr 0.113 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_gen_planes_other 0.004 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1128 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing