X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V4APDB ENTRY 2V4A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Microbatch under-oil5.52955% PEG Smear, 0.1M acetate, 10mM zinc acetate, pH 5.5, Microbatch under-oil, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.6253

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.25α = 90
b = 58.75β = 102.21
c = 105.16γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-06-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X120.932EMBL/DESY, HAMBURGX12

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
11.982593.40.06212.162.9755816868824.62
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)
11.982.0487.10.2014.32.54412

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2V4A1.9820.66867765243343493.450.218880.217040.25392RANDOM11.741
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]
-0.071.98-0.21.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.487
r_dihedral_angle_4_deg24.418
r_dihedral_angle_3_deg16.734
r_dihedral_angle_1_deg6.514
r_scangle_it3.327
r_scbond_it2.289
r_angle_other_deg2.263
r_angle_refined_deg1.813
r_mcangle_it1.393
r_mcbond_it0.852
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.487
r_dihedral_angle_4_deg24.418
r_dihedral_angle_3_deg16.734
r_dihedral_angle_1_deg6.514
r_scangle_it3.327
r_scbond_it2.289
r_angle_other_deg2.263
r_angle_refined_deg1.813
r_mcangle_it1.393
r_mcbond_it0.852
r_mcbond_other0.242
r_chiral_restr0.101
r_bond_refined_d0.02
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms6345
Nucleic Acid Atoms
Solvent Atoms468
Heterogen Atoms34

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction