X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1F41PDB entry 1F41

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.2 M CaCl2, 0.1 M HEPES pH 7.5, 28% PEG 400, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2946.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.388α = 90
b = 85.463β = 90
c = 64.233γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.4586LNLSW01B-MX2

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
11.830970.0633.726041
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)
1.81.840.0637.1

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 1F411.822.122267111497.470.2020.20.248RANDOM20.451
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]
-0.020.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.5
r_dihedral_angle_3_deg14.526
r_dihedral_angle_4_deg12.822
r_dihedral_angle_1_deg6.314
r_scangle_it2.052
r_angle_refined_deg1.375
r_scbond_it1.361
r_mcangle_it1.083
r_mcbond_it0.635
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.5
r_dihedral_angle_3_deg14.526
r_dihedral_angle_4_deg12.822
r_dihedral_angle_1_deg6.314
r_scangle_it2.052
r_angle_refined_deg1.375
r_scbond_it1.361
r_mcangle_it1.083
r_mcbond_it0.635
r_nbtor_refined0.309
r_symmetry_hbond_refined0.199
r_nbd_refined0.198
r_symmetry_vdw_refined0.178
r_xyhbond_nbd_refined0.144
r_chiral_restr0.101
r_bond_refined_d0.009
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1780
Nucleic Acid Atoms
Solvent Atoms207
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing