X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.829320 mM MgAc2, 100 mM MES, 13% MPD, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.6866.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.45α = 90
b = 299.75β = 112.6
c = 144.52γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2011-02-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
1330920.077411.62.821031019348522
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)
133.1940.5521.81

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 REPLACEMENTTHROUGHOUT1RYP315193484183809967592.080.1910.181530.180210.2068RANDOM58.534
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]
3.14-1.32-6.32.75
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.182
r_dihedral_angle_2_deg36.754
r_dihedral_angle_3_deg18.849
r_dihedral_angle_4_deg18.177
r_dihedral_angle_1_deg6.442
r_sphericity_bonded5.783
r_rigid_bond_restr1.826
r_angle_refined_deg1.125
r_angle_other_deg0.757
r_chiral_restr0.064
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.182
r_dihedral_angle_2_deg36.754
r_dihedral_angle_3_deg18.849
r_dihedral_angle_4_deg18.177
r_dihedral_angle_1_deg6.442
r_sphericity_bonded5.783
r_rigid_bond_restr1.826
r_angle_refined_deg1.125
r_angle_other_deg0.757
r_chiral_restr0.064
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49296
Nucleic Acid Atoms
Solvent Atoms281
Heterogen Atoms84

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing