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X-ray structure of human gankyrin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N1I SWISS-MODEL (PDB ENTRIES 1N1I, 1N0R, 1MJ0, 1N0Q) experimental model PDB 1N0R SWISS-MODEL (PDB ENTRIES 1N1I, 1N0R, 1MJ0, 1N0Q) experimental model PDB 1MJ0 SWISS-MODEL (PDB ENTRIES 1N1I, 1N0R, 1MJ0, 1N0Q) experimental model PDB 1N0Q SWISS-MODEL (PDB ENTRIES 1N1I, 1N0R, 1MJ0, 1N0Q)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 3.5M Na Formate , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 5.15 76.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.373 α = 90 b = 116.373 β = 90 c = 74.399 γ = 90
Symmetry Space Group P 41 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 IMAGE PLATE MARRESEARCH mirrors 2003-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 1.0000 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.8 20 99.8 0.072 0.072 35.4 13 12978
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 2.8 2.9 99.3 0.62 0.62 4
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT SWISS-MODEL
(PDB ENTRIES 1N1I, 1N0R, 1MJ0, 1N0Q) 2.8 20 12144 632 98.01 0.18748 0.1857 0.23349 0.2376 RANDOM 27.566
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] -1.74 -1.74 3.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.897 r_scangle_it 2.205 r_angle_refined_deg 1.281 r_scbond_it 1.224 r_angle_other_deg 1.037 r_mcangle_it 0.729 r_mcbond_it 0.375 r_symmetry_vdw_other 0.29 r_nbd_other 0.243 r_symmetry_hbond_refined 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.897 r_scangle_it 2.205 r_angle_refined_deg 1.281 r_scbond_it 1.224 r_angle_other_deg 1.037 r_mcangle_it 0.729 r_mcbond_it 0.375 r_symmetry_vdw_other 0.29 r_nbd_other 0.243 r_symmetry_hbond_refined 0.23 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.141 r_nbtor_other 0.082 r_chiral_restr 0.067 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1680 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing