X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3K9VPDB entry 3K9V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION728516% PEG 1000, 10% Jeffamine ED-2001, 20% glycerol, 0.1 M MES, pH 7.0, VAPOR DIFFUSION, temperature 285K
Crystal Properties
Matthews coefficientSolvent content
2.5752.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.45α = 90
b = 94.63β = 89.96
c = 113.5γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDRh coated flat mirror2010-01-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.979SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.5113.595.50.0680.0685.82762917629174.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.52.6497.50.4440.4441.6211367

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3K9V2.560.017625972447381294.90.2660.2660.281RANDOM65.893
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]
-66.06-11.869.1756.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.73
r_dihedral_angle_4_deg19.327
r_dihedral_angle_3_deg18.5
r_dihedral_angle_1_deg7.711
r_scangle_it3.953
r_scbond_it2.511
r_mcangle_it1.788
r_angle_refined_deg1.684
r_mcbond_it0.98
r_chiral_restr0.149
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.73
r_dihedral_angle_4_deg19.327
r_dihedral_angle_3_deg18.5
r_dihedral_angle_1_deg7.711
r_scangle_it3.953
r_scbond_it2.511
r_mcangle_it1.788
r_angle_refined_deg1.684
r_mcbond_it0.98
r_chiral_restr0.149
r_bond_refined_d0.019
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15616
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms304

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection