X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XMIPDB ENTRY 2XMI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
13.550MM NA-CITRATE PH 3.5, 2.9M AMMONIUM SULFATE, 10% PEG 550 MME
Crystal Properties
Matthews coefficientSolvent content
2.3347

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.43α = 90
b = 82.43β = 90
c = 86.31γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
12.13599.80.0419.983.8538236-3
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)
12.12.1599.80.562.53.83

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 2XMI2.171.436254198199.760.191620.189710.2275RANDOM71.987
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]
30.5830.58-61.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.387
r_dihedral_angle_4_deg22.379
r_dihedral_angle_3_deg16.349
r_dihedral_angle_1_deg6.667
r_scangle_it4.705
r_scbond_it3.391
r_mcangle_it2.609
r_mcbond_it1.668
r_angle_refined_deg1.554
r_angle_other_deg1.097
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.387
r_dihedral_angle_4_deg22.379
r_dihedral_angle_3_deg16.349
r_dihedral_angle_1_deg6.667
r_scangle_it4.705
r_scbond_it3.391
r_mcangle_it2.609
r_mcbond_it1.668
r_angle_refined_deg1.554
r_angle_other_deg1.097
r_mcbond_other0.481
r_symmetry_hbond_refined0.287
r_symmetry_vdw_refined0.255
r_symmetry_vdw_other0.249
r_nbd_refined0.212
r_nbtor_refined0.185
r_nbd_other0.184
r_xyhbond_nbd_refined0.181
r_chiral_restr0.125
r_xyhbond_nbd_other0.103
r_nbtor_other0.088
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
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 Atoms4977
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing