X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M5WPDB entry 1M5W

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.528916.4% PEG4000, 0.1 M Hepes NaOH, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2946.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.09α = 118.48
b = 91.864β = 116.81
c = 90.024γ = 93.5
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2008-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.97934APS24-ID-E

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
12.285096.50.10712.6273.791137
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)
12.282.3885.20.4812.138058

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 REPLACEMENTTHROUGHOUTPDB entry 1M5W2.2846.591104458094.20.1890.1860.245RANDOM28.325
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]
-0.580.93-0.840.49-0.65-1.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.406
r_dihedral_angle_4_deg19.242
r_dihedral_angle_3_deg15.597
r_dihedral_angle_1_deg5.375
r_scangle_it2.423
r_scbond_it1.389
r_angle_refined_deg1.152
r_mcangle_it0.91
r_angle_other_deg0.894
r_mcbond_it0.469
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.406
r_dihedral_angle_4_deg19.242
r_dihedral_angle_3_deg15.597
r_dihedral_angle_1_deg5.375
r_scangle_it2.423
r_scbond_it1.389
r_angle_refined_deg1.152
r_mcangle_it0.91
r_angle_other_deg0.894
r_mcbond_it0.469
r_mcbond_other0.077
r_chiral_restr0.065
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14763
Nucleic Acid Atoms
Solvent Atoms851
Heterogen Atoms64

Software

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