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Crystal structure of BchU complexed with S-adenosyl-L-homocysteine and Zn-bacteriopheophorbide d
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X1B PDB ENTRY 1X1B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1M TRIS, 1.5M ammonium sulfate, 12% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3 59.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.613 α = 90 b = 81.613 β = 90 c = 251.65 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD RIGAKU JUPITER 210 2004-11-27 M SINGLE WAVELENGTH 2 1 x-ray 93 CCD ADSC QUANTUM 4 2004-12-05 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.25 SPring-8 BL38B1 2 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.35 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 1,2 2.7 50 99.7 0.078 16.7 19.1 14488 3 71.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 2.7 2.8 99.7 0.32 15.6
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 (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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1X1B 2.7 46.99 13746 1392 95.1 0.242 0.237 0.237 0.236 0.286 0.2845 RANDOM 69.7
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] 15.45 16.41 15.45 -30.9
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.2 c_scangle_it 7.72 c_scbond_it 5.49 c_mcangle_it 5.48 c_mcbond_it 3.62 c_improper_angle_d 1.8 c_angle_deg 1.6 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.2 c_scangle_it 7.72 c_scbond_it 5.49 c_mcangle_it 5.48 c_mcbond_it 3.62 c_improper_angle_d 1.8 c_angle_deg 1.6 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2655 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 38
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing