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, 13% MPD, PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
3.6766.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.32α = 90
b = 300.9β = 112.81
c = 144.92γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2012-05-13MSINGLE 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
12.53098.90.05216.436698236294622
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)
12.52.692.30.4213.9

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 REPLACEMENTTHROUGHOUT1RYP2.51153629463447981814899.570.1980.194580.19330.2189RANDOM62.692
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]
4.65-1.74-5.891.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.447
r_sphericity_free27.536
r_sphericity_bonded16.48
r_dihedral_angle_3_deg14.411
r_dihedral_angle_4_deg14.342
r_dihedral_angle_1_deg5.173
r_long_range_B_refined3.239
r_long_range_B_other3.225
r_mcangle_it2.873
r_mcangle_other2.873
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.447
r_sphericity_free27.536
r_sphericity_bonded16.48
r_dihedral_angle_3_deg14.411
r_dihedral_angle_4_deg14.342
r_dihedral_angle_1_deg5.173
r_long_range_B_refined3.239
r_long_range_B_other3.225
r_mcangle_it2.873
r_mcangle_other2.873
r_scangle_other2.589
r_mcbond_it2.175
r_mcbond_other2.175
r_scbond_it2.123
r_scbond_other2.123
r_rigid_bond_restr1.84
r_angle_refined_deg0.899
r_angle_other_deg0.705
r_chiral_restr0.05
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49370
Nucleic Acid Atoms
Solvent Atoms426
Heterogen Atoms181

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing