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Crystal structure of PcyA-biliverdin complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 ammonium sulfate, sodium cacodylate, sodium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.6 51.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.826 α = 90 b = 94.997 β = 90 c = 42.675 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 2005-06-06 M SINGLE WAVELENGTH 2 1
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 1.51 50 99.6 0.078 7.8 45715 45715
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 1.51 1.56 98 98 0.335 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MIRAS THROUGHOUT 1.51 47.67 45672 45672 2304 99.59 0.158 0.158 0.157 0.1712 0.183 0.1644 RANDOM 17.216
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] 0.04 -0.06 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.163 r_dihedral_angle_4_deg 16.618 r_dihedral_angle_3_deg 13.526 r_dihedral_angle_1_deg 6.227 r_scangle_it 4.274 r_scbond_it 2.652 r_mcangle_it 1.829 r_angle_refined_deg 1.704 r_angle_other_deg 1.038 r_mcbond_it 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.163 r_dihedral_angle_4_deg 16.618 r_dihedral_angle_3_deg 13.526 r_dihedral_angle_1_deg 6.227 r_scangle_it 4.274 r_scbond_it 2.652 r_mcangle_it 1.829 r_angle_refined_deg 1.704 r_angle_other_deg 1.038 r_mcbond_it 1.03 r_mcbond_other 0.29 r_metal_ion_refined 0.247 r_nbd_refined 0.229 r_symmetry_vdw_other 0.223 r_xyhbond_nbd_refined 0.196 r_nbd_other 0.193 r_symmetry_hbond_refined 0.188 r_nbtor_refined 0.185 r_symmetry_vdw_refined 0.113 r_chiral_restr 0.1 r_nbtor_other 0.089 r_gen_planes_other 0.02 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1934 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 44
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS phasing CNS refinement REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction