X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XCDPDB ENTRY 2XCD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.514% PEG 3350, 0.1 M SODIUM MALONATE, 0.1 M, BIS-TRIS PROPANE PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.244.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.82α = 90
b = 100.01β = 90
c = 99.51γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2011-01-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

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
11.628.899.50.087.85.91315221
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)
11.61.6999.90.62.16.4

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 2XCD1.670.65123669657799.030.153470.15030.21365RANDOM21.005
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]
-0.09-0.440.53
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free33.817
r_dihedral_angle_2_deg33.52
r_dihedral_angle_4_deg18.007
r_dihedral_angle_3_deg13.532
r_sphericity_bonded12.439
r_dihedral_angle_1_deg6.081
r_rigid_bond_restr2.716
r_angle_refined_deg1.446
r_angle_other_deg0.841
r_chiral_restr0.082
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free33.817
r_dihedral_angle_2_deg33.52
r_dihedral_angle_4_deg18.007
r_dihedral_angle_3_deg13.532
r_sphericity_bonded12.439
r_dihedral_angle_1_deg6.081
r_rigid_bond_restr2.716
r_angle_refined_deg1.446
r_angle_other_deg0.841
r_chiral_restr0.082
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6273
Nucleic Acid Atoms
Solvent Atoms1137
Heterogen Atoms125

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling