X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WL9PDB ENTRY 1WL9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.2277HANGING DROP VAPOUR DIFFUSION AT 4C. 2 UL 6 MG/ML APPRO PLUS 2 UL RESERVOIR SOLUTION: 28 % PEG 4K, 0.1 M TRIS PH 8.2. SOAKED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 10% MPD AND 1 MM MNCL2 FOR 1 HR AT 4C PRIOR TO CRYOCOOLING.
Crystal Properties
Matthews coefficientSolvent content
4.471.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.147α = 90
b = 177.147β = 90
c = 96.438γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOSMIC MIRRORS2005-06-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200H

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
11.7576.797.30.0617.4586631621.28
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)
11.751.8497.90.293.43.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1WL91.7560.0883997263296.80.150.150.165RANDOM21.82
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]
-0.08-0.04-0.080.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.013
r_dihedral_angle_4_deg13.591
r_dihedral_angle_3_deg10.95
r_sphericity_free6.609
r_dihedral_angle_1_deg5.83
r_scangle_it5.202
r_scbond_it3.611
r_mcangle_it2.043
r_mcbond_it1.855
r_angle_refined_deg1.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.013
r_dihedral_angle_4_deg13.591
r_dihedral_angle_3_deg10.95
r_sphericity_free6.609
r_dihedral_angle_1_deg5.83
r_scangle_it5.202
r_scbond_it3.611
r_mcangle_it2.043
r_mcbond_it1.855
r_angle_refined_deg1.16
r_angle_other_deg0.787
r_mcbond_other0.423
r_symmetry_vdw_other0.297
r_symmetry_vdw_refined0.227
r_nbd_refined0.206
r_nbd_other0.176
r_nbtor_refined0.173
r_xyhbond_nbd_refined0.119
r_symmetry_hbond_refined0.119
r_nbtor_other0.078
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3495
Nucleic Acid Atoms
Solvent Atoms642
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling