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DypB N246A in complex with manganese
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VEE PDB ENTRY 3VEE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 295 0.1 M sodium acetate trihydrate, pH 4.5, 3 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.62 66.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.96 α = 90 b = 132.96 β = 90 c = 159.502 γ = 120
Symmetry Space Group P 32 2 1
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 315r 2011-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.97530 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.2 115.146 99.8 0.065 19.6 7 82867 82867
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 100 0.376 0.376 1.9 7.1 12001
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 PDB ENTRY 3VEE 2.2 41.56 82785 4142 99.69 0.1687 0.1673 0.1951 0.19 RANDOM 36.1644
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] -0.06 -0.06 -0.06 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.433 r_dihedral_angle_4_deg 20.014 r_dihedral_angle_3_deg 13.47 r_dihedral_angle_1_deg 5.679 r_angle_refined_deg 1.377 r_chiral_restr 0.102 r_bond_refined_d 0.01 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7006 Nucleic Acid Atoms Solvent Atoms 655 Heterogen Atoms 144
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection REFMAC phasing