X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RKSpdb entries 1RKS, 1VM7
experimental modelPDB 1VM7pdb entries 1RKS, 1VM7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29140% PEG-550MME, vapor diffusion, sitting drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.346.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.53α = 90
b = 72.978β = 91.08
c = 90.958γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.000APS17-ID

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
12.15099.30.04613.6334881
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)
12.12.1897.80.2613

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entries 1RKS, 1VM72.13034605177099.1860.2010.2010.19790.2484thin shells23.979
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]
-0.083-0.0180.0620.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.534
r_dihedral_angle_4_deg16.233
r_dihedral_angle_3_deg12.543
r_dihedral_angle_1_deg4.528
r_scangle_it2.561
r_scbond_it1.537
r_angle_refined_deg1.462
r_scangle_other1.286
r_mcangle_it0.926
r_angle_other_deg0.914
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.534
r_dihedral_angle_4_deg16.233
r_dihedral_angle_3_deg12.543
r_dihedral_angle_1_deg4.528
r_scangle_it2.561
r_scbond_it1.537
r_angle_refined_deg1.462
r_scangle_other1.286
r_mcangle_it0.926
r_angle_other_deg0.914
r_mcbond_it0.493
r_mcangle_other0.424
r_scbond_other0.325
r_symmetry_vdw_other0.223
r_symmetry_vdw_refined0.221
r_nbd_refined0.206
r_symmetry_hbond_refined0.192
r_nbd_other0.183
r_nbtor_refined0.168
r_xyhbond_nbd_refined0.154
r_metal_ion_refined0.11
r_mcbond_other0.104
r_nbtor_other0.086
r_chiral_restr0.082
r_bond_refined_d0.017
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4524
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms70

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction