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Crystal structure of the dark-adapted full-length bacteriophytochrome XccBphP mutant D199A from Xanthomonas campestris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AKP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.9 293 7%(W/V) PEG 4000
0.2 M SODIUM ACETATE
0.1 M TRIS
Crystal Properties Matthews coefficient Solvent content 3.21 61.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.86 α = 90 b = 103.86 β = 90 c = 342.61 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 Convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors 2016-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9801 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 3.45 48.94 100 0.165 0.172 0.048 0.99 10.6 12.4 25772 2 124.23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.45 3.69 100 1.536 1.605 0.459 0.69 1.7 12
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 5AKP 3.45 47.27 25682 1258 100 0.231 0.23 0.2517 0.25 0.2743 RANDOM 134.73
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] 1.6451 1.6451 -3.2902
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 4.09 t_omega_torsion 2.71 t_angle_deg 1.19 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 4.09 t_omega_torsion 2.71 t_angle_deg 1.19 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9367 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 86
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing