X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QLAPDB entry 2QLA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529325% PEG2000, 0.2 M NaCl, 0.1 M TRIS, 3.3 mM NiCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6854.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.339α = 90
b = 107.396β = 105.52
c = 102.051γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing)2008-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.97607SSRLBL9-1

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
12.498.53397.20.0960.0966.4642.7563115548522
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)
12.42.53970.5520.5521.32.68079

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 DIFFRACTIONTHROUGHOUTPDB entry 2QLA2.498.535721455103398096.310.2130.2130.2090.268RANDOM41.455
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]
0.10.11-0.150.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.25
r_dihedral_angle_3_deg19.263
r_dihedral_angle_4_deg13.467
r_dihedral_angle_1_deg5.06
r_scangle_it1.714
r_angle_refined_deg1.246
r_scbond_it1.142
r_mcangle_it0.63
r_mcbond_it0.37
r_nbtor_other0.324
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.25
r_dihedral_angle_3_deg19.263
r_dihedral_angle_4_deg13.467
r_dihedral_angle_1_deg5.06
r_scangle_it1.714
r_angle_refined_deg1.246
r_scbond_it1.142
r_mcangle_it0.63
r_mcbond_it0.37
r_nbtor_other0.324
r_angle_other_deg0.317
r_nbtor_refined0.278
r_symmetry_vdw_refined0.223
r_symmetry_hbond_refined0.215
r_nbd_refined0.199
r_xyhbond_nbd_refined0.14
r_nbd_other0.093
r_chiral_restr0.075
r_mcbond_other0.046
r_metal_ion_refined0.018
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9648
Nucleic Acid Atoms
Solvent Atoms119
Heterogen Atoms756

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOLREPphasing