X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4A6PPDB ENTRY 4A6P

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.860 MM NAPHOSPHATE PH 5.8, 15% PEG1000
Crystal Properties
Matthews coefficientSolvent content
2.1543

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.308α = 90
b = 87.13β = 90.55
c = 62.322γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-12-10MSINGLE 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
11.8843.5699.10.110.443.51347732
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)
11.881.9996.60.52.613.47

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 4A6P1.8862.3233051171999.20.174160.171240.2314RANDOM22.423
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]
1.85-0.34-2.060.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.121
r_dihedral_angle_4_deg17.171
r_dihedral_angle_3_deg13.909
r_dihedral_angle_1_deg6.184
r_mcangle_it2.993
r_scbond_it2.651
r_mcbond_it1.898
r_mcbond_other1.895
r_angle_refined_deg1.792
r_angle_other_deg1.087
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.121
r_dihedral_angle_4_deg17.171
r_dihedral_angle_3_deg13.909
r_dihedral_angle_1_deg6.184
r_mcangle_it2.993
r_scbond_it2.651
r_mcbond_it1.898
r_mcbond_other1.895
r_angle_refined_deg1.792
r_angle_other_deg1.087
r_chiral_restr0.107
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.004
r_gen_planes_other0.004
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_it
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 Atoms3472
Nucleic Acid Atoms
Solvent Atoms496
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
AMoREphasing