1T6F

Crystal Structure of the Coiled-coil Dimerization Motif of Geminin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1E7TPDB ENTRY 1E7T

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529110% PEG 6000, 5% MPD, 100 mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.0941.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 25.12α = 90
b = 43.44β = 90
c = 67.5γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHosmic mirrors2003-06-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54180

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.4436.5292.81397912978
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.441.5288.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1E7T1.47251167460193.380.18070.18060.178670.22103RANDOM13.095
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]
-1.130.770.35
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it4.007
r_sphericity_free3.311
r_dihedral_angle_1_deg2.73
r_scbond_it2.384
r_sphericity_bonded1.793
r_mcangle_it1.503
r_rigid_bond_restr1.191
r_angle_refined_deg1.151
r_mcbond_it0.941
r_angle_other_deg0.725
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it4.007
r_sphericity_free3.311
r_dihedral_angle_1_deg2.73
r_scbond_it2.384
r_sphericity_bonded1.793
r_mcangle_it1.503
r_rigid_bond_restr1.191
r_angle_refined_deg1.151
r_mcbond_it0.941
r_angle_other_deg0.725
r_symmetry_vdw_other0.299
r_nbd_other0.227
r_nbd_refined0.221
r_xyhbond_nbd_refined0.119
r_symmetry_vdw_refined0.114
r_symmetry_hbond_refined0.108
r_nbtor_other0.083
r_chiral_restr0.06
r_gen_planes_other0.011
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms626
Nucleic Acid Atoms
Solvent Atoms125
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
EPMRphasing