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Crystal Structure of Pd(ally)/apo-C126AFr
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DAT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 ammonium sulfate, cadmium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.16 61.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.984 α = 90 b = 181.984 β = 90 c = 181.984 γ = 90
Symmetry Space Group F 4 3 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 CCD ADSC QUANTUM 210 2008-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.00 SPring-8 BL38B1
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 1.66 30 100 0.049 11.5 31026 14.263
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) 1.66 1.72 100 0.175 11.1
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 1DAT 1.66 27.76 29411 1563 99.95 0.18155 0.18082 0.1795 0.1952 0.1947 RANDOM 12.227
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 35.231 r_sphericity_free 17.721 r_dihedral_angle_4_deg 17.65 r_dihedral_angle_3_deg 12.598 r_sphericity_bonded 6.362 r_dihedral_angle_1_deg 4.32 r_scangle_it 3.342 r_scbond_it 2.076 r_mcangle_it 1.207 r_angle_refined_deg 1.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.231 r_sphericity_free 17.721 r_dihedral_angle_4_deg 17.65 r_dihedral_angle_3_deg 12.598 r_sphericity_bonded 6.362 r_dihedral_angle_1_deg 4.32 r_scangle_it 3.342 r_scbond_it 2.076 r_mcangle_it 1.207 r_angle_refined_deg 1.074 r_mcbond_it 0.734 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.213 r_metal_ion_refined 0.137 r_xyhbond_nbd_refined 0.136 r_symmetry_metal_ion_refined 0.13 r_symmetry_hbond_refined 0.111 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1378 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 44
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement SCALEPACK data scaling