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Crystal structure of I86D mutant of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin (data 3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QCD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 sodium citrate, sodium chloride, Tris
Crystal Properties Matthews coefficient Solvent content 2.55 53.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.823 α = 90 b = 95.861 β = 90 c = 42.378 γ = 90
Symmetry Space Group P 21 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 CCD RIGAKU JUPITER 210 2010-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.800 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.05 56.97 99.5 0.065 9.7 4.2 134801
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.05 1.09 99.3 0.378 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 4QCD 1.05 10 127522 127522 100 0.1388 0.142 0.1677 0.1415 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 36 2314.9
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.1622 s_zero_chiral_vol 0.0917 s_non_zero_chiral_vol 0.0878 s_similar_adp_cmpnt 0.0498 s_anti_bump_dis_restr 0.0367 s_angle_d 0.0316 s_bond_d 0.0146
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2042 Nucleic Acid Atoms Solvent Atoms 368 Heterogen Atoms 43
Software Software Software Name Purpose SHELXL-97 refinement PHENIX phasing HKL-2000 data reduction HKL-2000 data scaling SHELX phasing