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Y201W mutant of the orange carotenoid protein from Synechocystis at pH 4.6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XB5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.6 293 0.1 M Sodium acetate pH4.6
8 % w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.4 48.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.996 α = 90 b = 82.996 β = 90 c = 88.123 γ = 120
Symmetry Space Group P 32 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 EIGER X 16M 2019-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.976250 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.4 42 100 0.033 1 41.4 20 69390
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 100 1.164 0.882 3.5 20.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4XB5 1.4 41.5 65885 3461 99.9 0.1303 0.1284 0.1368 0.1665 0.1721 RANDOM 29.823
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] 0.54 0.27 0.54 -1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.097 r_dihedral_angle_4_deg 21.348 r_rigid_bond_restr 20.229 r_dihedral_angle_3_deg 11.339 r_dihedral_angle_1_deg 5.943 r_angle_other_deg 1.469 r_angle_refined_deg 1.354 r_chiral_restr 0.068 r_bond_other_d 0.009 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.097 r_dihedral_angle_4_deg 21.348 r_rigid_bond_restr 20.229 r_dihedral_angle_3_deg 11.339 r_dihedral_angle_1_deg 5.943 r_angle_other_deg 1.469 r_angle_refined_deg 1.354 r_chiral_restr 0.068 r_bond_other_d 0.009 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2347 Nucleic Acid Atoms Solvent Atoms 382 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing