X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OV8PDB entry 2OV8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52950.1M Bis-Tris propane pH6.5,0.2M NaI, 18% PEG 3350, 10mM PAP, 5mM desulfo-A47934, vapor diffusion, hanging drop, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.957.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.392α = 90
b = 87.392β = 90
c = 169.377γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4mirrors2005-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X8C1.1NSLSX8C

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
12.955099.90.04817.411.28661
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)
12.953.061000.53211.2825

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 2OV82.9576.92860541899.810.2260.2240.269RANDOM63.151
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]
-0.12-0.06-0.120.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.554
r_dihedral_angle_4_deg26.459
r_dihedral_angle_3_deg19.857
r_dihedral_angle_1_deg7.104
r_scangle_it2.476
r_angle_refined_deg1.614
r_scbond_it1.515
r_mcangle_it1.176
r_mcbond_it0.678
r_symmetry_hbond_refined0.333
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.554
r_dihedral_angle_4_deg26.459
r_dihedral_angle_3_deg19.857
r_dihedral_angle_1_deg7.104
r_scangle_it2.476
r_angle_refined_deg1.614
r_scbond_it1.515
r_mcangle_it1.176
r_mcbond_it0.678
r_symmetry_hbond_refined0.333
r_symmetry_vdw_refined0.326
r_nbtor_refined0.317
r_nbd_refined0.251
r_xyhbond_nbd_refined0.207
r_chiral_restr0.102
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1873
Nucleic Acid Atoms
Solvent Atoms12
Heterogen Atoms27

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction