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Crystal structure of DNPH1 (RCL) with kinetine riboside monophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FYI PDB ENTRY 4FYI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 291 100 MM TRIS, 1.2 M AMMONIUM SULPHATE, 20MM MGCL2, PH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.238 α = 90 b = 95.449 β = 101.56 c = 79.288 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 CCD MARMOSAIC 225 mm CCD 2011-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87260 ESRF ID23-2
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 1.9 29.97 98.6 0.086 7.9 2.2 36476 1
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 1.9 2 96.6 0.356 2.1 2.1
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 4FYI 1.9 23.86 36376 1818 98.33 0.2348 0.2322 0.2316 0.286 0.2866 RANDOM 17.2637
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] 0.07 0.09 0.23 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.294 r_dihedral_angle_3_deg 18.927 r_dihedral_angle_4_deg 15.032 r_dihedral_angle_1_deg 5.381 r_angle_refined_deg 1.896 r_scangle_it 1.676 r_scbond_it 1.129 r_mcangle_it 0.67 r_mcbond_it 0.377 r_chiral_restr 0.186
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.294 r_dihedral_angle_3_deg 18.927 r_dihedral_angle_4_deg 15.032 r_dihedral_angle_1_deg 5.381 r_angle_refined_deg 1.896 r_scangle_it 1.676 r_scbond_it 1.129 r_mcangle_it 0.67 r_mcbond_it 0.377 r_chiral_restr 0.186 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4043 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 116
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction