X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SMLPDB ENTRY 1SML

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5280AS, SOAKED CRYSTAL IN 5 ML DROP WITH CRYSTALLIZATION CONDITIONS AND 0.005 M EDTA FOR 30 MINUTES, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Crystal Properties
Matthews coefficientSolvent content
2.5451.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.22α = 90
b = 104.22β = 90
c = 195.74γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plateXenocs multilayers2006-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.819.7497.70.0960.0965.76.6572352
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.997.70.4680.3721.65.8

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 1SML1.819.7454307290997.350.17350.171580.20981RANDOM15.145
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]
0.080.040.08-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.396
r_dihedral_angle_4_deg15.221
r_dihedral_angle_3_deg13.65
r_dihedral_angle_1_deg7.605
r_scangle_it3.343
r_scbond_it2.091
r_angle_refined_deg1.404
r_mcangle_it1.211
r_mcbond_it0.753
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.396
r_dihedral_angle_4_deg15.221
r_dihedral_angle_3_deg13.65
r_dihedral_angle_1_deg7.605
r_scangle_it3.343
r_scbond_it2.091
r_angle_refined_deg1.404
r_mcangle_it1.211
r_mcbond_it0.753
r_nbtor_refined0.309
r_nbd_refined0.291
r_symmetry_vdw_refined0.211
r_symmetry_hbond_refined0.185
r_xyhbond_nbd_refined0.151
r_chiral_restr0.091
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4049
Nucleic Acid Atoms
Solvent Atoms674
Heterogen Atoms32

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4model building
REFMACrefinement
XDSdata reduction
CCP4data scaling
CCP4phasing