X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.530020%peg5k mme, bis-tris 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.3447.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.045α = 90
b = 55.323β = 90
c = 124.308γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS V2006-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.862.14933058030580
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.8662.7

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 REPLACEMENTTHROUGHOUT1VYH1.862.142904629046154493.230.1510.1510.1490.192RANDOM14.759
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]
-0.170.49-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.601
r_dihedral_angle_4_deg13.691
r_dihedral_angle_3_deg12.188
r_dihedral_angle_1_deg7.152
r_scangle_it2.937
r_scbond_it1.824
r_angle_refined_deg1.277
r_mcangle_it1.036
r_mcbond_it0.628
r_nbtor_refined0.296
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.601
r_dihedral_angle_4_deg13.691
r_dihedral_angle_3_deg12.188
r_dihedral_angle_1_deg7.152
r_scangle_it2.937
r_scbond_it1.824
r_angle_refined_deg1.277
r_mcangle_it1.036
r_mcbond_it0.628
r_nbtor_refined0.296
r_symmetry_vdw_refined0.196
r_nbd_refined0.195
r_xyhbond_nbd_refined0.127
r_symmetry_hbond_refined0.127
r_chiral_restr0.093
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2485
Nucleic Acid Atoms
Solvent Atoms484
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
HKL-2000data scaling
MOLREPphasing