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 MgCl2, 0.1 M TRIS, 3.3 mM NiCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.5465.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.897α = 90
b = 104.897β = 90
c = 107.925γ = 120
Symmetry
Space GroupP 63 2 2

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
13107.8331000.1510.1514.713.17479747922
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)
33.161000.60.61.213.41053

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 2QLA390.917569746151999.890.2250.2250.2210.277RANDOM43.31
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]
0.030.010.03-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.203
r_dihedral_angle_3_deg22.529
r_dihedral_angle_4_deg20.209
r_dihedral_angle_1_deg5.064
r_scangle_it2.154
r_angle_refined_deg1.441
r_scbond_it1.235
r_mcangle_it0.932
r_mcbond_it0.521
r_nbtor_refined0.291
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.203
r_dihedral_angle_3_deg22.529
r_dihedral_angle_4_deg20.209
r_dihedral_angle_1_deg5.064
r_scangle_it2.154
r_angle_refined_deg1.441
r_scbond_it1.235
r_mcangle_it0.932
r_mcbond_it0.521
r_nbtor_refined0.291
r_symmetry_vdw_refined0.266
r_nbd_refined0.232
r_symmetry_hbond_refined0.159
r_xyhbond_nbd_refined0.118
r_chiral_restr0.089
r_bond_refined_d0.013
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1608
Nucleic Acid Atoms
Solvent Atoms20
Heterogen Atoms126

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction