X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LZ0PDB ENTRY 1LZ0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
172981% PEG4000, 5% MPD, 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM ADA, pH 7.6, 30 mM sodium acetate, pH 4.6, 5 mM manganese chloride, with 20% MPD as cryoprotectant, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.346.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.71α = 90
b = 149.44β = 90
c = 79.95γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXISOSMIC BLUE MIRRORS2008-05-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0021.54

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
11.8674.74493.80.055134.5525287
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)
11.861.9396.20.343.34.232555

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 1LZ01.862025285128393.760.19290.19040.2389RANDOM27.5985
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]
-0.140.73-0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.209
r_dihedral_angle_4_deg15.878
r_dihedral_angle_3_deg15.77
r_dihedral_angle_1_deg6.693
r_scangle_it4.975
r_scbond_it3.285
r_angle_refined_deg2.036
r_mcangle_it1.978
r_mcbond_it1.244
r_chiral_restr0.154
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.209
r_dihedral_angle_4_deg15.878
r_dihedral_angle_3_deg15.77
r_dihedral_angle_1_deg6.693
r_scangle_it4.975
r_scbond_it3.285
r_angle_refined_deg2.036
r_mcangle_it1.978
r_mcbond_it1.244
r_chiral_restr0.154
r_bond_refined_d0.026
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2393
Nucleic Acid Atoms
Solvent Atoms278
Heterogen Atoms45

Software

Software
Software NamePurpose
d*TREKdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata scaling
MOLREPphasing