X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5295Protein solution: 7.7 mg/mL, 0.25M Sodium chloride, 0.01M Tris-HCl (pH 8.3), Screen solution: PEG's II, condition D10, 0.2M Sodium acetate, 0.1M Tris (pH 8.5), 30% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.935.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.666α = 90
b = 125.217β = 105.73
c = 79.472γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBeryllium lenses2009-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
12.6301000.10312.63.84580445804-345.4
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)
12.62.641000.5092.73.82277

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 REPLACEMENTTHROUGHOUT1EJD2.629.884324243242229999.960.18360.18360.17980.25472RANDOM32.778
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]
0.70.45-0.02-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg22.47
r_dihedral_angle_4_deg9.342
r_dihedral_angle_3_deg8.892
r_scangle_it5.506
r_scbond_it3.296
r_mcangle_it1.937
r_dihedral_angle_1_deg1.612
r_angle_refined_deg1.27
r_mcbond_it1.02
r_angle_other_deg0.772
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg22.47
r_dihedral_angle_4_deg9.342
r_dihedral_angle_3_deg8.892
r_scangle_it5.506
r_scbond_it3.296
r_mcangle_it1.937
r_dihedral_angle_1_deg1.612
r_angle_refined_deg1.27
r_mcbond_it1.02
r_angle_other_deg0.772
r_mcbond_other0.312
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12624
Nucleic Acid Atoms
Solvent Atoms494
Heterogen Atoms23

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling