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Crystal structure of PcyA-biliverdin XIII alpha complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D1E PDB ENTRY 2D1E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 2.0M ammonium sulfate, 0.2M sodium chloride, 0.1M sodium cacodylate (pH 7.0), vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.54 51.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.785 α = 90 b = 94.797 β = 90 c = 42.653 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 ADSC QUANTUM 315 2006-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.7085 SPring-8 BL41XU
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 1.04 28.94 99.4 0.048 6 134142
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) 1.04 1.08 98.9 0.279 4.7
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 DIFFERENCE FOURIER PDB ENTRY 2D1E 1.04 28.94 134142 134142 0.125 0.125 0.1752 0.148 0.1822 RANDOM 19.363
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]
RMS Deviations Key Refinement Restraint Deviation s_angle_d 2.75 s_bond_d 0.027 s_similar_dist s_from_restr_planes s_zero_chiral_vol s_non_zero_chiral_vol s_anti_bump_dis_restr s_rigid_bond_adp_cmpnt s_similar_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3471 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 48
Software Software Software Name Purpose SHELX refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling SHELXL refinement