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Crystal structure of CDP-Chase in complex with Gd3+
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 Tris-HCl, Li2SO4, PEG-4000, pH 8.5, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.55 51.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.005 α = 90 b = 70.855 β = 90 c = 111.793 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2007-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.54178
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 2.5 50 95.5 0.083 15.7 4.6 16640
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 2.5 2.59 97.9 0.544 4.5 1664
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 Direct refinement THROUGHOUT 2.5 43.9 16610 846 95.43 0.2258 0.2225 0.2096 0.2876 0.2717 RANDOM 51.6056
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] 0.82 0.42 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.582 r_dihedral_angle_4_deg 16.985 r_dihedral_angle_3_deg 16.089 r_dihedral_angle_1_deg 6.104 r_scangle_it 2.448 r_scbond_it 1.618 r_mcangle_it 1.273 r_angle_refined_deg 1.162 r_mcbond_it 0.945 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.582 r_dihedral_angle_4_deg 16.985 r_dihedral_angle_3_deg 16.089 r_dihedral_angle_1_deg 6.104 r_scangle_it 2.448 r_scbond_it 1.618 r_mcangle_it 1.273 r_angle_refined_deg 1.162 r_mcbond_it 0.945 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.208 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.174 r_symmetry_hbond_refined 0.142 r_metal_ion_refined 0.102 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3326 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 3
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction REFMAC phasing