X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QXMpdb entry 1QXM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529820% PEG 4000, 15% isopropanol, 200 mM Li2SO4, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.140

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.084α = 90
b = 146.595β = 90
c = 35.712γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSCMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.9179SSRLBL9-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.525870.06613.68865422
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.51.53978.60.2993.788654

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 1QXM1.521.22173397382087.090.169040.167710.19445RANDOM19.526
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]
0.02-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.222
r_dihedral_angle_4_deg15.771
r_dihedral_angle_3_deg11.572
r_dihedral_angle_1_deg7.273
r_scangle_it2.563
r_scbond_it1.863
r_angle_refined_deg1.239
r_mcangle_it1.068
r_mcbond_it0.858
r_angle_other_deg0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.222
r_dihedral_angle_4_deg15.771
r_dihedral_angle_3_deg11.572
r_dihedral_angle_1_deg7.273
r_scangle_it2.563
r_scbond_it1.863
r_angle_refined_deg1.239
r_mcangle_it1.068
r_mcbond_it0.858
r_angle_other_deg0.74
r_symmetry_vdw_other0.272
r_symmetry_vdw_refined0.233
r_nbd_refined0.217
r_nbd_other0.189
r_nbtor_refined0.18
r_mcbond_other0.165
r_symmetry_hbond_refined0.139
r_xyhbond_nbd_refined0.135
r_nbtor_other0.083
r_chiral_restr0.078
r_xyhbond_nbd_other0.024
r_bond_refined_d0.009
r_bond_other_d0.006
r_gen_planes_refined0.005
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4677
Nucleic Acid Atoms
Solvent Atoms564
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement