X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W85PDB entry 1W85

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5291.15The protein solution was then mixed in 1:1 volume ratio of crystallization buffer consisting of 8-12 % mono-methyl ether polyethylene glycol (MME PEG) 5000, 0.1 M Na maleate pH 5.5, and the droplet was left to equilibrate against a reservoir of neat crystallization buffer., VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
Crystal Properties
Matthews coefficientSolvent content
1.8633.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.247α = 90
b = 231.995β = 90.74
c = 92.614γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirror2005-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.9795ESRFID23-1

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
12.56698.90.1110.1113.13.799540993512.62.6
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)
2.52.6499.90.260.3025.43.7

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1W852.559.449432494324502798.860.192330.188480.26303RANDOM42.879
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]
2.230.06-0.31-1.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.56
r_dihedral_angle_4_deg17.147
r_dihedral_angle_3_deg13.013
r_scangle_it10.492
r_scbond_it8.418
r_mcangle_it5.28
r_mcbond_it3.954
r_angle_refined_deg1.282
r_dihedral_angle_1_deg1.161
r_nbtor_refined0.327
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.56
r_dihedral_angle_4_deg17.147
r_dihedral_angle_3_deg13.013
r_scangle_it10.492
r_scbond_it8.418
r_mcangle_it5.28
r_mcbond_it3.954
r_angle_refined_deg1.282
r_dihedral_angle_1_deg1.161
r_nbtor_refined0.327
r_symmetry_vdw_refined0.259
r_nbd_refined0.244
r_xyhbond_nbd_refined0.146
r_chiral_restr0.133
r_symmetry_hbond_refined0.125
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms21953
Nucleic Acid Atoms
Solvent Atoms407
Heterogen Atoms123

Software

Software
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing