X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WPHPDB entry 1WPH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52930.1 M NH4 Citrate, 0.1 % w/v NDSB 256, 5 % w/v PEG 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1442.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.595α = 90
b = 135.595β = 90
c = 54.936γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315LN2 cooled first crystal, sagital focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror, beam defining slits2006-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97937APS19-ID

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
12501000.0660.0669.64.42543725437-345.7
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)
122.0782.70.5630.56324.4

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1WPH2.140.13199711997110280.1960.1960.1930.26RANDOM41.53
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]
-0.13-0.06-0.130.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.108
r_dihedral_angle_4_deg17.821
r_dihedral_angle_3_deg15.351
r_dihedral_angle_1_deg6.341
r_scangle_it3.615
r_scbond_it2.411
r_angle_refined_deg1.908
r_mcangle_it1.45
r_mcbond_it0.983
r_angle_other_deg0.902
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.108
r_dihedral_angle_4_deg17.821
r_dihedral_angle_3_deg15.351
r_dihedral_angle_1_deg6.341
r_scangle_it3.615
r_scbond_it2.411
r_angle_refined_deg1.908
r_mcangle_it1.45
r_mcbond_it0.983
r_angle_other_deg0.902
r_symmetry_vdw_refined0.337
r_symmetry_vdw_other0.33
r_mcbond_other0.276
r_nbd_refined0.238
r_nbtor_refined0.19
r_nbd_other0.183
r_xyhbond_nbd_refined0.168
r_symmetry_hbond_refined0.145
r_chiral_restr0.104
r_nbtor_other0.093
r_bond_refined_d0.022
r_gen_planes_refined0.007
r_bond_other_d0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2724
Nucleic Acid Atoms
Solvent Atoms53
Heterogen Atoms53

Software

Software
Software NamePurpose
HKL-3000data collection
HKL-3000data reduction
REFMACrefinement
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing