X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WN0PDB ENTRY 1WN0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.529310 MG/ML PROTEIN, 1.0 M SODIUM CITRATE, 0.10 M PIPES, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
2.855.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.558α = 90
b = 100.558β = 90
c = 69.568γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDAPS-1SAGITALLY FOCUSING 2ND CRYSTAL, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR2004-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BMAPS19-BM

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
1237.7798.90.10516.7478.424495
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)
22.0599.50.5963.5217.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1WN0237.7723200124998.950.1750.175250.172460.2272RANDOM23.782
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]
0.110.11-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.971
r_dihedral_angle_4_deg21.838
r_dihedral_angle_3_deg14.908
r_scangle_it8.329
r_scbond_it5.61
r_dihedral_angle_1_deg5.033
r_mcangle_it3.53
r_mcbond_it2.939
r_angle_refined_deg1.609
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.971
r_dihedral_angle_4_deg21.838
r_dihedral_angle_3_deg14.908
r_scangle_it8.329
r_scbond_it5.61
r_dihedral_angle_1_deg5.033
r_mcangle_it3.53
r_mcbond_it2.939
r_angle_refined_deg1.609
r_nbtor_refined0.308
r_nbd_refined0.214
r_symmetry_vdw_refined0.191
r_symmetry_hbond_refined0.189
r_xyhbond_nbd_refined0.167
r_chiral_restr0.118
r_bond_refined_d0.02
r_gen_planes_refined0.008
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 Atoms2183
Nucleic Acid Atoms
Solvent Atoms319
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
ARP/wARPmodel building