X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GSFPDB entry 2GSF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529820 mg/mL Protein, 25% PEG 3350, 0.2M Ammonium sulfate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9737.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.59α = 90
b = 38.098β = 101.72
c = 76.031γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATERIGAKU RAXIS IV2006-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT

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
11.6526.4995.80.03148.86.835314
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)
1.651.764.50.13412.56.4

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 2GSF1.6526.4935314180196.640.170.1690.196RANDOM16.354
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.383
r_dihedral_angle_4_deg14.398
r_dihedral_angle_3_deg11.64
r_dihedral_angle_1_deg5.144
r_scangle_it2.38
r_scbond_it1.641
r_angle_refined_deg1.134
r_mcangle_it1.01
r_mcbond_it0.89
r_angle_other_deg0.838
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.383
r_dihedral_angle_4_deg14.398
r_dihedral_angle_3_deg11.64
r_dihedral_angle_1_deg5.144
r_scangle_it2.38
r_scbond_it1.641
r_angle_refined_deg1.134
r_mcangle_it1.01
r_mcbond_it0.89
r_angle_other_deg0.838
r_symmetry_hbond_refined0.294
r_symmetry_vdw_other0.231
r_xyhbond_nbd_refined0.229
r_nbd_refined0.213
r_nbd_other0.18
r_nbtor_refined0.172
r_symmetry_vdw_refined0.172
r_mcbond_other0.148
r_nbtor_other0.08
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2387
Nucleic Acid Atoms
Solvent Atoms304
Heterogen Atoms4

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling