X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XDMPDB ENTRY 2XDM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16pH 6
Crystal Properties
Matthews coefficientSolvent content
2.6653.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.234α = 90
b = 92.284β = 94.2
c = 107.105γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH SX-165MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30AESRFBM30A

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
12.641.392.70.0612.13.257773
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)
12.62.7483.80.382.73

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 2XDM2.638.954750295792.30.1970.1940.262RANDOM64.5
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]
0.07-0.10.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.138
r_dihedral_angle_3_deg17.66
r_dihedral_angle_4_deg15.504
r_dihedral_angle_1_deg6.483
r_scangle_it2.882
r_scbond_it1.823
r_angle_refined_deg1.458
r_mcangle_it1.442
r_mcbond_it0.784
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.138
r_dihedral_angle_3_deg17.66
r_dihedral_angle_4_deg15.504
r_dihedral_angle_1_deg6.483
r_scangle_it2.882
r_scbond_it1.823
r_angle_refined_deg1.458
r_mcangle_it1.442
r_mcbond_it0.784
r_chiral_restr0.09
r_bond_refined_d0.013
r_gen_planes_refined0.006
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_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 Atoms13394
Nucleic Acid Atoms
Solvent Atoms247
Heterogen Atoms157

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling