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Crystal structure of APC complexed with Asef
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NMW 3NMW, 2PZ1 experimental model PDB 2PZ1 3NMW, 2PZ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 277 1M lithium sulfate, 0.5M ammonium sulfate, pH 5.6, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.9 74.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.175 α = 90 b = 163.175 β = 90 c = 242.593 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 2010-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.000 Photon Factory BL-17A
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 3 50 96.1 0.057 15.1 5.6 46293
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 3 3.11 69.2 0.406 4.3 3347
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 3NMW, 2PZ1 3.01 50 43230 2202 90.24 0.2505 0.2487 0.2485 0.2839 0.2852 RANDOM 82.824
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] -0.01 -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.634 r_dihedral_angle_3_deg 17.616 r_dihedral_angle_4_deg 16.088 r_dihedral_angle_1_deg 4.1 r_angle_refined_deg 0.861 r_scangle_it 0.416 r_scbond_it 0.24 r_mcangle_it 0.144 r_mcbond_it 0.072 r_chiral_restr 0.057
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.634 r_dihedral_angle_3_deg 17.616 r_dihedral_angle_4_deg 16.088 r_dihedral_angle_1_deg 4.1 r_angle_refined_deg 0.861 r_scangle_it 0.416 r_scbond_it 0.24 r_mcangle_it 0.144 r_mcbond_it 0.072 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7546 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction