X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4MLEPDB entry 4MLE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7300100 mM Hepes, pH 7.0, 28% PEG 1500, 5% glycerol, 50 mM glucose, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.8156.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.116α = 90
b = 80.116β = 90
c = 321.807γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rRh coated flat mirror2010-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-10.97946SSRLBL7-1

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
12.329.1999.90.1250.1198.089.992845828432
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)
12.32.421000.2850.2852.810.424054

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 4MLE2.329.192845426901142999.830.233050.231210.26748RANDOM58.174
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]
1.020.511.02-3.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.006
r_dihedral_angle_4_deg20.933
r_dihedral_angle_3_deg18.405
r_long_range_B_refined8.802
r_dihedral_angle_1_deg5.786
r_mcangle_it5.202
r_scbond_it4.551
r_mcbond_it3.547
r_angle_refined_deg1.351
r_chiral_restr0.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.006
r_dihedral_angle_4_deg20.933
r_dihedral_angle_3_deg18.405
r_long_range_B_refined8.802
r_dihedral_angle_1_deg5.786
r_mcangle_it5.202
r_scbond_it4.551
r_mcbond_it3.547
r_angle_refined_deg1.351
r_chiral_restr0.094
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3505
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms39

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
CrystalCleardata reduction
SCALAdata scaling