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Crystal structure of PcyA-181,182-dihydrobiliverdin complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D1E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.85M sodium citrate, 0.1M sodium cacodylate (pH 7.0), vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.56 51.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.822 α = 90 b = 95.087 β = 90 c = 42.782 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 2007-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 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 1.48 35.42 95.3 0.066 3.5 46254
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) 1.48 1.56 97.9 0.307 3.4
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 DIFFERENCE FOURIER THROUGHOUT 2D1E 1.48 35.42 46226 2341 94.44 0.166 0.164 0.1727 0.197 0.2039 RANDOM 19.449
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 r_dihedral_angle_2_deg 36.609 r_dihedral_angle_4_deg 15.843 r_dihedral_angle_3_deg 13.819 r_dihedral_angle_1_deg 6.209 r_scangle_it 3.587 r_scbond_it 2.463 r_angle_refined_deg 1.901 r_mcangle_it 1.501 r_mcbond_it 1.322 r_angle_other_deg 1.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.609 r_dihedral_angle_4_deg 15.843 r_dihedral_angle_3_deg 13.819 r_dihedral_angle_1_deg 6.209 r_scangle_it 3.587 r_scbond_it 2.463 r_angle_refined_deg 1.901 r_mcangle_it 1.501 r_mcbond_it 1.322 r_angle_other_deg 1.125 r_mcbond_other 0.256 r_symmetry_vdw_other 0.246 r_nbd_refined 0.219 r_nbd_other 0.203 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.171 r_symmetry_hbond_refined 0.17 r_symmetry_vdw_refined 0.152 r_chiral_restr 0.09 r_nbtor_other 0.089 r_gen_planes_other 0.02 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2066 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling