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Crystal Structure of HasAp with Gallium Phthalocyanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W8O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.91M MgSO4, 50mM MES (pH5.6), 50mM KPi (pH7.0)
Crystal Properties Matthews coefficient Solvent content 3.31 62.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.625 α = 90 b = 153.625 β = 90 c = 36.761 γ = 120
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 RAYONIX MX-225 2014-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.5 50 98.5 0.106 0.121 0.056 8.2 4.2 17415
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 99.4 0.358 0.421 0.217 0.825 3.1 861
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 MOLECULAR REPLACEMENT THROUGHOUT 3W8O 2.5 38.41 16300 871 97.12 0.1927 0.1902 0.1966 0.2383 0.2409 RANDOM 36.261
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 35.49 r_dihedral_angle_3_deg 15.551 r_dihedral_angle_4_deg 7.938 r_dihedral_angle_1_deg 6.683 r_angle_refined_deg 1.567 r_angle_other_deg 1.028 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_bond_other_d 0.007 r_gen_planes_refined 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.49 r_dihedral_angle_3_deg 15.551 r_dihedral_angle_4_deg 7.938 r_dihedral_angle_1_deg 6.683 r_angle_refined_deg 1.567 r_angle_other_deg 1.028 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_bond_other_d 0.007 r_gen_planes_refined 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2659 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement DENZO data collection SCALEPACK data scaling PDB_EXTRACT data extraction DENZO data reduction MOLREP phasing