X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1P5F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529830% PEG 3000, 100 mM HEPES, 200 mM NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.856.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.842α = 90
b = 66.842β = 90
c = 175.852γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATERIGAKU RAXIS IV++2007-09-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.542

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
11.8557.9399.80.09931.113.62077820778
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)
1.851.921000.0753.514.52025

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 REPLACEMENTTHROUGHOUT1P5F1.85501965619656106499.870.183460.183460.181330.2263RANDOM21.541
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]
0.030.010.03-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.365
r_dihedral_angle_4_deg18.326
r_dihedral_angle_3_deg11.947
r_dihedral_angle_1_deg5.894
r_scangle_it3.351
r_scbond_it2.09
r_angle_refined_deg1.339
r_mcangle_it1.218
r_mcbond_it0.791
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.365
r_dihedral_angle_4_deg18.326
r_dihedral_angle_3_deg11.947
r_dihedral_angle_1_deg5.894
r_scangle_it3.351
r_scbond_it2.09
r_angle_refined_deg1.339
r_mcangle_it1.218
r_mcbond_it0.791
r_nbtor_refined0.3
r_symmetry_vdw_refined0.209
r_nbd_refined0.202
r_symmetry_hbond_refined0.163
r_xyhbond_nbd_refined0.145
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1420
Nucleic Acid Atoms
Solvent Atoms189
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing