X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LZ7PDB ENTRY 1LZ7

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
2.2846.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.59α = 90
b = 149.84β = 90
c = 79.44γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXISOSMIC BLUE MIRRORS2008-05-07MSINGLE 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
11.4974.95395.50.03220.64.2849296
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)
11.491.5493.50.2654.13.584771

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 1LZ71.492049296249695.460.19530.19380.2214RANDOM21.0097
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]
-0.270.3-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.599
r_dihedral_angle_4_deg18.316
r_dihedral_angle_3_deg14.379
r_dihedral_angle_1_deg6.693
r_scangle_it5.618
r_scbond_it3.803
r_angle_refined_deg2.562
r_mcangle_it2.465
r_mcbond_it1.539
r_chiral_restr0.175
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.599
r_dihedral_angle_4_deg18.316
r_dihedral_angle_3_deg14.379
r_dihedral_angle_1_deg6.693
r_scangle_it5.618
r_scbond_it3.803
r_angle_refined_deg2.562
r_mcangle_it2.465
r_mcbond_it1.539
r_chiral_restr0.175
r_bond_refined_d0.032
r_gen_planes_refined0.016
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2254
Nucleic Acid Atoms
Solvent Atoms267
Heterogen Atoms45

Software

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