X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GZ1PDB Entry: 2GZ1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629350 mM Citrate pH 6.0 200 mM ammonium acetate 20% PEG 8000 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3246.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.348α = 89.98
b = 64.439β = 81.06
c = 96.739γ = 82
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2006-01-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

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
12.343.5892.70.1136.63.39573522
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)
12.32.3889.60.2933.33.315581

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: 2GZ12.130.017501075010376991.680.2140.2140.2110.277RANDOM22.018
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]
0.27-0.03-0.04-0.01-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.697
r_dihedral_angle_4_deg17.199
r_dihedral_angle_3_deg16.158
r_dihedral_angle_1_deg6.103
r_scangle_it2.285
r_scbond_it1.444
r_angle_refined_deg1.334
r_mcangle_it0.846
r_mcbond_it0.511
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.697
r_dihedral_angle_4_deg17.199
r_dihedral_angle_3_deg16.158
r_dihedral_angle_1_deg6.103
r_scangle_it2.285
r_scbond_it1.444
r_angle_refined_deg1.334
r_mcangle_it0.846
r_mcbond_it0.511
r_nbtor_refined0.3
r_nbd_refined0.197
r_symmetry_vdw_refined0.162
r_xyhbond_nbd_refined0.157
r_symmetry_hbond_refined0.145
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10759
Nucleic Acid Atoms
Solvent Atoms808
Heterogen Atoms224

Software

Software
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata reduction
PHASERphasing