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CRYSTAL STRUCTURE OF C-MYB R2R3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MBG PDB ENTRIES 1MBG AND 1MBJ experimental model PDB 1MBJ PDB ENTRIES 1MBG AND 1MBJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.8 1.6-1.7 M SODIUM CITRATE PH 6.8, PROTEIN CONCENTRATION 15 MG/ML, CRYSTAL WAS GROWN BY REPEATED MACROSEEDING, TRANSFORMED TO LOW HUMIDITY FORM AND FLASH COOLED, 1-2% V/V OF GLYCEROL WAS ADDED TO SODIUM CITRATE TO PREVENT THE CRYSTAL CRACKING DURING THE FLASH COOLING
Crystal Properties Matthews coefficient Solvent content 1.9 35.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.722 α = 90 b = 28.25 β = 90.87 c = 44.129 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE RIGAKU RAXIS IV 1998-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 SPring-8 BL44B2
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 1.68 50 99.1 0.1 12.601 4.244 11033 13.4
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 1.68 1.74 97.9 0.446 1.904 3.53
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRIES 1MBG AND 1MBJ 1.68 44.12 11022 570 98.8 0.193 0.193 0.21 RANDOM 18.3
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] 1.6 0.64 0.17 -1.77
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.5 c_scangle_it 4.92 c_scbond_it 3.21 c_mcangle_it 2.5 c_mcbond_it 1.74 c_angle_deg 1.3 c_improper_angle_d 0.8 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.5 c_scangle_it 4.92 c_scbond_it 3.21 c_mcangle_it 2.5 c_mcbond_it 1.74 c_angle_deg 1.3 c_improper_angle_d 0.8 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 867 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 2
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling X-PLOR phasing