X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
170.2M CACL2, 16% PEG 6K, 0.1M HEPES PH7
Crystal Properties
Matthews coefficientSolvent content
2.2645.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.116α = 90
b = 99.345β = 90
c = 99.252γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2009-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
11.8535.0899.90.0115.69.4841931
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)
11.851.951000.942.47.4

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 2XCD1.851078928456399.90.1530.1510.187RANDOM16.05
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]
0.38-0.05-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.392
r_dihedral_angle_4_deg15.995
r_dihedral_angle_3_deg15.141
r_dihedral_angle_1_deg6.897
r_scangle_it4.608
r_scbond_it2.97
r_angle_refined_deg2.007
r_mcangle_it1.995
r_mcbond_it1.191
r_angle_other_deg1.044
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.392
r_dihedral_angle_4_deg15.995
r_dihedral_angle_3_deg15.141
r_dihedral_angle_1_deg6.897
r_scangle_it4.608
r_scbond_it2.97
r_angle_refined_deg2.007
r_mcangle_it1.995
r_mcbond_it1.191
r_angle_other_deg1.044
r_mcbond_other0.38
r_chiral_restr0.126
r_bond_refined_d0.024
r_gen_planes_refined0.01
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_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 Atoms6300
Nucleic Acid Atoms
Solvent Atoms792
Heterogen Atoms212

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing