X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QP8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5293100mM Sodium citrate pH5.0, 200mM Ammonium sulfate, 22% v/v PEG 10000
Crystal Properties
Matthews coefficientSolvent content
3.261.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.326α = 90
b = 102.618β = 103.53
c = 101.287γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HEhorizontal focusing mirror2013-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.90000SPring-8BL44XU

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
12.75501000.0919.14.142426
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)
12.752.81000.7594.12105

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2QP82.7549.1842403213999.720.1830.17950.2517RANDOM54.999
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]
0.010.04-0.030.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.228
r_dihedral_angle_4_deg18.823
r_dihedral_angle_3_deg17.214
r_dihedral_angle_1_deg8.092
r_mcangle_it6.655
r_mcbond_other4.074
r_mcbond_it4.073
r_angle_refined_deg1.695
r_angle_other_deg0.987
r_chiral_restr0.087
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.228
r_dihedral_angle_4_deg18.823
r_dihedral_angle_3_deg17.214
r_dihedral_angle_1_deg8.092
r_mcangle_it6.655
r_mcbond_other4.074
r_mcbond_it4.073
r_angle_refined_deg1.695
r_angle_other_deg0.987
r_chiral_restr0.087
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9283
Nucleic Acid Atoms
Solvent Atoms43
Heterogen Atoms90

Software

Software
Software NamePurpose
DENZOdata collection
SCALEPACKdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPmodel building
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing