X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PEEPDB ENTRY 1PEE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5298sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.6826.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.526α = 90
b = 34.526β = 90
c = 255.76γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315bent Si-mirror2004-08-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9APS14-BM-C

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
11.718.5299.10.07204.9183161831634.7
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)
1.71.7699.20.3823.81792

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1PEE1.718.52172461724691799.150.18330.18330.181130.22551RANDOM23.485
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]
-0.19-0.190.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.888
r_dihedral_angle_3_deg13.981
r_dihedral_angle_4_deg9.184
r_dihedral_angle_1_deg6.991
r_scangle_it3.779
r_sphericity_bonded3.259
r_scbond_it2.833
r_mcangle_it1.915
r_angle_refined_deg1.911
r_mcbond_it1.644
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.888
r_dihedral_angle_3_deg13.981
r_dihedral_angle_4_deg9.184
r_dihedral_angle_1_deg6.991
r_scangle_it3.779
r_sphericity_bonded3.259
r_scbond_it2.833
r_mcangle_it1.915
r_angle_refined_deg1.911
r_mcbond_it1.644
r_angle_other_deg1.428
r_mcbond_other0.35
r_symmetry_vdw_other0.237
r_nbd_refined0.184
r_nbd_other0.18
r_nbtor_refined0.174
r_xyhbond_nbd_refined0.158
r_symmetry_hbond_refined0.158
r_symmetry_vdw_refined0.14
r_chiral_restr0.121
r_nbtor_other0.088
r_bond_refined_d0.021
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1432
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
XDISPLAYFdata reduction
d*TREKdata scaling