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Crystal structure of LOV1 D33N mutant of phototropin from Klebsormidium nitens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8I11
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289.15 sodium phoshate monobasic monohydrate , potassium phosphate dibasic , pH 8.2
Crystal Properties Matthews coefficient Solvent content 2.91 57.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.451 α = 90 b = 53.451 β = 90 c = 138.514 γ = 90
Symmetry Space Group P 43 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 EIGER X 9M 2022-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.918402 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.08 49.867 95.1 0.997 10.8 20 12100
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.081 6.622 0.997
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.081 49.867 9452 476 74.128 0.172 0.1699 0.1828 0.211 0.2105 31.488
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] -0.18 -0.18 0.361
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.775 r_dihedral_angle_6_deg 14.87 r_dihedral_angle_2_deg 10.689 r_lrange_it 8.665 r_lrange_other 8.463 r_dihedral_angle_1_deg 7.376 r_scangle_it 5.758 r_scangle_other 5.754 r_mcangle_other 4.747 r_mcangle_it 4.744
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.775 r_dihedral_angle_6_deg 14.87 r_dihedral_angle_2_deg 10.689 r_lrange_it 8.665 r_lrange_other 8.463 r_dihedral_angle_1_deg 7.376 r_scangle_it 5.758 r_scangle_other 5.754 r_mcangle_other 4.747 r_mcangle_it 4.744 r_scbond_other 3.626 r_scbond_it 3.618 r_mcbond_it 2.913 r_mcbond_other 2.912 r_angle_refined_deg 1.452 r_angle_other_deg 0.462 r_xyhbond_nbd_refined 0.257 r_nbd_refined 0.24 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.188 r_symmetry_xyhbond_nbd_refined 0.174 r_symmetry_nbd_refined 0.162 r_nbd_other 0.155 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 916 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing