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apo-H49AFr with high content of Pd ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DAT PDB ENTRY 1DAT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Ammonium sulfate, Cadmium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.11 60.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.701 α = 90 b = 180.701 β = 90 c = 180.701 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 RIGAKU JUPITER 210 2008-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 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 1.8 30 100 0.089 57.4 11.6 24004
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) 1.8 1.86 100 0.3 8 11.4
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 PDB ENTRY 1DAT 1.8 21.3 22765 1228 99.95 0.19712 0.19566 0.1939 0.22526 0.2238 RANDOM 20.797
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 35.17 r_dihedral_angle_4_deg 23.442 r_dihedral_angle_3_deg 14.917 r_dihedral_angle_1_deg 4.706 r_scangle_it 3.742 r_scbond_it 2.46 r_mcangle_it 1.468 r_angle_refined_deg 1.252 r_mcbond_it 0.996 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.17 r_dihedral_angle_4_deg 23.442 r_dihedral_angle_3_deg 14.917 r_dihedral_angle_1_deg 4.706 r_scangle_it 3.742 r_scbond_it 2.46 r_mcangle_it 1.468 r_angle_refined_deg 1.252 r_mcbond_it 0.996 r_nbtor_refined 0.303 r_nbd_refined 0.23 r_symmetry_vdw_refined 0.204 r_metal_ion_refined 0.168 r_xyhbond_nbd_refined 0.159 r_symmetry_hbond_refined 0.159 r_symmetry_metal_ion_refined 0.121 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1406 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 14
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement SCALEPACK data scaling