X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GNYPDB ENTRY 3GNY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529830% MPD; 0.1 M HEPES sodium pH 7.5; 0.2 M sodium citrate dihydrate , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.141.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.6α = 90
b = 31.024β = 90
c = 39.726γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2009-02-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54

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
11.5639.726990.050.06324.96.78427841611
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)
11.561.6294.40.0960.105256.3776

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3GNY1.56208019840939099.890.1690.170.1690.198RANDOM13.777
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]
0.18-0.07-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.077
r_dihedral_angle_3_deg13.086
r_dihedral_angle_4_deg10.936
r_dihedral_angle_1_deg7.361
r_scangle_it3.531
r_scbond_it2.105
r_angle_refined_deg1.663
r_mcangle_it1.539
r_mcbond_it0.928
r_chiral_restr0.112
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.077
r_dihedral_angle_3_deg13.086
r_dihedral_angle_4_deg10.936
r_dihedral_angle_1_deg7.361
r_scangle_it3.531
r_scbond_it2.105
r_angle_refined_deg1.663
r_mcangle_it1.539
r_mcbond_it0.928
r_chiral_restr0.112
r_bond_refined_d0.014
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms460
Nucleic Acid Atoms
Solvent Atoms81
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing