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Crystal Structure of the Coiled-coil Dimerization Motif of Geminin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E7T PDB ENTRY 1E7T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 10% PEG 6000, 5% MPD, 100 mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.09 41.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.12 α = 90 b = 43.44 β = 90 c = 67.5 γ = 90
Symmetry Space Group P 21 21 21
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 osmic mirrors 2003-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54180
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.44 36.52 92.8 13979 12978
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.44 1.52 88.9
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 (All) 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 1E7T 1.47 25 11674 601 93.38 0.1807 0.1806 0.17867 0.1965 0.22103 0.2461 RANDOM 13.095
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] -1.13 0.77 0.35
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.007 r_sphericity_free 3.311 r_dihedral_angle_1_deg 2.73 r_scbond_it 2.384 r_sphericity_bonded 1.793 r_mcangle_it 1.503 r_rigid_bond_restr 1.191 r_angle_refined_deg 1.151 r_mcbond_it 0.941 r_angle_other_deg 0.725
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.007 r_sphericity_free 3.311 r_dihedral_angle_1_deg 2.73 r_scbond_it 2.384 r_sphericity_bonded 1.793 r_mcangle_it 1.503 r_rigid_bond_restr 1.191 r_angle_refined_deg 1.151 r_mcbond_it 0.941 r_angle_other_deg 0.725 r_symmetry_vdw_other 0.299 r_nbd_other 0.227 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.119 r_symmetry_vdw_refined 0.114 r_symmetry_hbond_refined 0.108 r_nbtor_other 0.083 r_chiral_restr 0.06 r_gen_planes_other 0.011 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 626 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling EPMR phasing