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Crystal structure of Ps i-CgsB in complex with k-i-k-neocarrahexaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HDH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.65 291 PEG 3350, citric acid, arginine
Crystal Properties Matthews coefficient Solvent content 2.97 58.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.39 α = 90 b = 123.39 β = 90 c = 240.11 γ = 90
Symmetry Space Group P 43 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 PIXEL DECTRIS PILATUS 6M 2014-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97949 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.5 109.8 0.174 0.067 0.992 63124
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 97.7 0.78 0.311 0.778 2.5 6.9 9074
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 1HDH 2.5 109.75 59927 3136 97.2 0.2155 0.2145 0.219 0.2337 0.2361 RANDOM 27.894
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] -0.03 -0.03 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.958 r_dihedral_angle_4_deg 14.972 r_dihedral_angle_3_deg 12.813 r_dihedral_angle_1_deg 5.973 r_angle_refined_deg 1.391 r_angle_other_deg 0.956 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.958 r_dihedral_angle_4_deg 14.972 r_dihedral_angle_3_deg 12.813 r_dihedral_angle_1_deg 5.973 r_angle_refined_deg 1.391 r_angle_other_deg 0.956 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10625 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 376
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing PDB_EXTRACT data extraction