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Primase large subunit amino terminal domain from Pyrococcus horikoshii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other seleno-methionie derivative structure(This is not deposited to PDB)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 1M Ammonium Sulfate, 50mM Magnesium Sulfate, 25mM Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.2 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.25 α = 90 b = 89.25 β = 90 c = 252.674 γ = 90
Symmetry Space Group P 43 21 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 MAR CCD 165 mm 2003-07-07 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MAR CCD 165 mm 2003-10-21 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU 2 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.9793, 0.9795, 0.9840, 0.9717 SPring-8 BL41XU
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 1,2 2.9 50 99.2 0.044 17 7.2 23616 23431 2 2 56.447
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) 1,2 2.9 2.93 100 0.218 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD, MOLECULAR REPLACEMENT THROUGHOUT seleno-methionie derivative structure(This is not deposited to PDB) 2.9 20 2 23360 22869 21250 0.2482 0.2404 0.3094 0.2392 RANDOM 26.3411
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] -5 -5 10.001
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.49354 c_angle_deg 1.36362 c_improper_angle_d 0.79216 c_bond_d 0.00829
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5272 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data reduction MLPHARE phasing CNS refinement HKL-2000 data scaling