X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FRVPDB ENTRY 2FRV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.3293PEG8000, sodium chloride, N,N-dimethyl dodecylamine N-oxide, glycerol, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.30
Crystal Properties
Matthews coefficientSolvent content
2.345.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.75α = 89.33
b = 93.44β = 102.41
c = 69.03γ = 90.95
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH1996-08-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.3519.886.20.0698.41.85863937.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.4578.2

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 2FRV2.35136144758485296292.20.1350.1320.183RANDOM14.54
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]
2.37-1.110.020.130.9-2.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.337
r_dihedral_angle_4_deg19.189
r_dihedral_angle_3_deg17.933
r_dihedral_angle_1_deg5.397
r_scangle_it2.52
r_scbond_it1.969
r_mcangle_it1.473
r_mcbond_it1.157
r_angle_refined_deg1.088
r_nbtor_refined0.324
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.337
r_dihedral_angle_4_deg19.189
r_dihedral_angle_3_deg17.933
r_dihedral_angle_1_deg5.397
r_scangle_it2.52
r_scbond_it1.969
r_mcangle_it1.473
r_mcbond_it1.157
r_angle_refined_deg1.088
r_nbtor_refined0.324
r_symmetry_hbond_refined0.282
r_nbd_refined0.233
r_xyhbond_nbd_refined0.158
r_symmetry_vdw_refined0.158
r_chiral_restr0.082
r_bond_refined_d0.009
r_gen_planes_refined0.004
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 Atoms12237
Nucleic Acid Atoms
Solvent Atoms515
Heterogen Atoms114

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ProDCdata collection
XDSdata scaling
AMoREphasing