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, 0.8 % w/v NDSB 256, 5 % w/v PEG 3350, 1 % v/v Glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1843.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.136α = 90
b = 136.136β = 90
c = 55.418γ = 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)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
12.1501000.08185.12223822238-341.5
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)
12.12.14840.4232.85.1

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 1WPH2.140.39216082160811020.1960.1960.1940.247RANDOM26.96
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]
-0.28-0.14-0.280.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.212
r_dihedral_angle_4_deg17.153
r_dihedral_angle_3_deg15.286
r_dihedral_angle_1_deg6.623
r_scangle_it3.518
r_scbond_it2.406
r_angle_refined_deg1.842
r_mcangle_it1.36
r_angle_other_deg0.932
r_mcbond_it0.926
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.212
r_dihedral_angle_4_deg17.153
r_dihedral_angle_3_deg15.286
r_dihedral_angle_1_deg6.623
r_scangle_it3.518
r_scbond_it2.406
r_angle_refined_deg1.842
r_mcangle_it1.36
r_angle_other_deg0.932
r_mcbond_it0.926
r_symmetry_vdw_other0.32
r_mcbond_other0.276
r_nbd_refined0.232
r_symmetry_vdw_refined0.206
r_nbtor_refined0.189
r_nbd_other0.181
r_xyhbond_nbd_refined0.169
r_chiral_restr0.102
r_nbtor_other0.092
r_symmetry_hbond_refined0.081
r_bond_refined_d0.02
r_bond_other_d0.009
r_gen_planes_refined0.008
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 Atoms2741
Nucleic Acid Atoms
Solvent Atoms42
Heterogen Atoms51

Software

Software
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
REFMACrefinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing