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Albumin-dexamethasone complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V08
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 289 Prior to crystallization, 15 mg/ml protein was incubated with dexamethasone powder (10-fold molar excess) for 60 min at room temperature, and the mixture with the powder in suspension was used for crystallization. 1 ul of this mixture was mixed with 1 ul of the well condition (1.8 M ammonium dihydrogen citrate, pH 7.0) and equilibrated against the well solution in 15-Well hanging drop crystallization plate (Qiagen, EasyXtal). 1:1 mixture of Paratone N and mineral oil was used as a cryoprotectant
Crystal Properties Matthews coefficient Solvent content 2.84 56.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.983 α = 90 b = 94.983 β = 90 c = 143.591 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 MARMOSAIC 225 mm CCD 2011-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.979 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.4 50 99.8 0.11 0.123 0.055 8.8 4.9 28870 -3 40
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 98.3 1.053 1.221 0.605 0.619 3.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3V08 2.4 47.54 22871 1132 83.67 0.2054 0.2033 0.2492 0.2605 RANDOM 56.799
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] -0.05 -0.02 -0.05 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.544 r_dihedral_angle_4_deg 17.818 r_dihedral_angle_3_deg 13.695 r_dihedral_angle_1_deg 4.967 r_angle_other_deg 1.148 r_angle_refined_deg 1.127 r_chiral_restr 0.041 r_bond_other_d 0.003 r_bond_refined_d 0.002 r_gen_planes_refined 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.544 r_dihedral_angle_4_deg 17.818 r_dihedral_angle_3_deg 13.695 r_dihedral_angle_1_deg 4.967 r_angle_other_deg 1.148 r_angle_refined_deg 1.127 r_chiral_restr 0.041 r_bond_other_d 0.003 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4589 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 61
Software Software Software Name Purpose HKL-3000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction MOLREP phasing SCALEPACK data scaling Coot model building