X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PHCPDB entry 2PHC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.929315% PEG 8000, 20% glycerol, 40mM potassium phosphate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6152.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.909α = 90
b = 84.417β = 90
c = 84.409γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateOsmic mirror optics2008-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
131799.80.146.7667516738-3-378
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
33.1198.40.661.54.6629

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 2PHC3.0116.886399637532199.630.267470.267470.263540.34378RANDOM37.673
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]
3.09-1.64-1.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.906
r_dihedral_angle_3_deg20.449
r_dihedral_angle_4_deg11.555
r_dihedral_angle_1_deg7.222
r_scangle_it4.474
r_scbond_it3.013
r_mcangle_it2.188
r_mcbond_it1.271
r_angle_refined_deg1.219
r_angle_other_deg0.882
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.906
r_dihedral_angle_3_deg20.449
r_dihedral_angle_4_deg11.555
r_dihedral_angle_1_deg7.222
r_scangle_it4.474
r_scbond_it3.013
r_mcangle_it2.188
r_mcbond_it1.271
r_angle_refined_deg1.219
r_angle_other_deg0.882
r_symmetry_hbond_refined0.293
r_mcbond_other0.251
r_nbd_refined0.214
r_nbd_other0.185
r_nbtor_refined0.185
r_symmetry_vdw_other0.182
r_xyhbond_nbd_refined0.161
r_symmetry_vdw_refined0.118
r_symmetry_hbond_other0.1
r_nbtor_other0.089
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1635
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing