X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YDGPDB entry 1YDG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.829315-35 % PEG 1500, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.6873.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.361α = 90
b = 94.361β = 90
c = 175.363γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHmirrors2006-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X121.0EMBL/DESY, HAMBURGX12

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
11.665098.70.1212.16.3929839177422
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.661.6997.30.682.25.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 1YDG1.6629.4128922986954460997.450.169880.169020.18573RANDOM29.749
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]
0.040.04-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.145
r_dihedral_angle_4_deg15.26
r_dihedral_angle_3_deg12.9
r_dihedral_angle_1_deg5.397
r_scangle_it3.137
r_scbond_it1.954
r_angle_refined_deg1.328
r_mcangle_it1.161
r_mcbond_it0.742
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.145
r_dihedral_angle_4_deg15.26
r_dihedral_angle_3_deg12.9
r_dihedral_angle_1_deg5.397
r_scangle_it3.137
r_scbond_it1.954
r_angle_refined_deg1.328
r_mcangle_it1.161
r_mcbond_it0.742
r_nbtor_refined0.303
r_symmetry_hbond_refined0.261
r_nbd_refined0.203
r_symmetry_vdw_refined0.186
r_xyhbond_nbd_refined0.162
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2916
Nucleic Acid Atoms
Solvent Atoms463
Heterogen Atoms140

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing