X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.3ROOM TEMPERATURE HANGING DROP WITH 16% PEG4K, 0.1 M TRIS (PH8.3), 0.2 M MGCL2. CRYOPROTECTED WITH 10-15% MPD., pH 8.30
Crystal Properties
Matthews coefficientSolvent content
4.468.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.974α = 90
b = 236.703β = 106.14
c = 137.637γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOSMIC MIRRORS2004-05-21MSINGLE 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
12.329.9798.90.0617.622.8150167-3.735.89
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)
12.32.3897.60.323.42.7

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 1WL92.329.97142654751298.90.1680.1670.197RANDOM35.06
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]
1.450.94-0.1-0.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.327
r_dihedral_angle_4_deg16.933
r_dihedral_angle_3_deg12.294
r_scangle_it7.246
r_dihedral_angle_1_deg5.706
r_scbond_it5.156
r_mcangle_it3.238
r_mcbond_it2.57
r_angle_refined_deg1.07
r_angle_other_deg0.763
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.327
r_dihedral_angle_4_deg16.933
r_dihedral_angle_3_deg12.294
r_scangle_it7.246
r_dihedral_angle_1_deg5.706
r_scbond_it5.156
r_mcangle_it3.238
r_mcbond_it2.57
r_angle_refined_deg1.07
r_angle_other_deg0.763
r_symmetry_vdw_other0.265
r_symmetry_vdw_refined0.199
r_nbd_refined0.197
r_nbd_other0.172
r_nbtor_refined0.17
r_xyhbond_nbd_refined0.132
r_symmetry_hbond_refined0.102
r_nbtor_other0.079
r_chiral_restr0.062
r_bond_refined_d0.009
r_gen_planes_refined0.003
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_mcbond_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_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13964
Nucleic Acid Atoms
Solvent Atoms832
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing