X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2I2BPDB ENTRY 2i2b

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.40.3 M potassium chloride, 50 mM tri-sodium citrate dihydrate, 15-20% w/v polyethylene glycol 400, pH 5.4, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.3447.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.481α = 90
b = 75.851β = 90
c = 118.35γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.933ESRFID23-1

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
12.2237.996.80.05422.94.9137801338338.5
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)
12.222.3481.20.4113.54

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 2i2b2.2237.93137801338340596.570.2080.2080.2070.252RANDOM34.883
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]
0.681.85-2.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.036
r_dihedral_angle_4_deg15.371
r_dihedral_angle_3_deg15.103
r_dihedral_angle_1_deg9.347
r_angle_refined_deg2.257
r_scangle_it1.502
r_scbond_it1.116
r_angle_other_deg0.958
r_mcangle_it0.778
r_mcbond_it0.472
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.036
r_dihedral_angle_4_deg15.371
r_dihedral_angle_3_deg15.103
r_dihedral_angle_1_deg9.347
r_angle_refined_deg2.257
r_scangle_it1.502
r_scbond_it1.116
r_angle_other_deg0.958
r_mcangle_it0.778
r_mcbond_it0.472
r_chiral_restr0.339
r_symmetry_hbond_refined0.335
r_nbtor_refined0.316
r_symmetry_vdw_refined0.293
r_nbd_refined0.218
r_xyhbond_nbd_refined0.194
r_nbtor_other0.116
r_nbd_other0.063
r_bond_refined_d0.012
r_bond_other_d0.004
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1979
Nucleic Acid Atoms
Solvent Atoms59
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing