X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GEHPDB ENTRY 1GEH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62930.1M Acetate, 0.1M CaCl2, 5% PEG6000, 10% MPD, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.160.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 173.287α = 90
b = 246.377β = 90
c = 144.589γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2102008-06-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.000SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (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
12.35099.90.10515.227196226.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.32.341000.3793.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1GEH2.335.392577311363099.550.201160.198870.24429RANDOM25.083
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]
4.52-2.27-2.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.821
r_dihedral_angle_4_deg19.538
r_dihedral_angle_3_deg14.192
r_dihedral_angle_1_deg5.23
r_scangle_it2.142
r_scbond_it1.274
r_angle_refined_deg0.995
r_mcangle_it0.822
r_mcbond_it0.421
r_chiral_restr0.068
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.821
r_dihedral_angle_4_deg19.538
r_dihedral_angle_3_deg14.192
r_dihedral_angle_1_deg5.23
r_scangle_it2.142
r_scbond_it1.274
r_angle_refined_deg0.995
r_mcangle_it0.822
r_mcbond_it0.421
r_chiral_restr0.068
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms34125
Nucleic Acid Atoms
Solvent Atoms2306
Heterogen Atoms220

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing