X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SRQPDB ENTRY 1SRQ for Rap1GAP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52858-11% PEG 2000 MME, 100mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties
Matthews coefficientSolvent content
5.06180475.700363

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 209.723α = 90
b = 209.723β = 90
c = 108.217γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-07-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.97916SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
13.4182.5799.20.0870.08715.486.537639376393-3
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)
3.43.598.40.3353.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1SRQ for Rap1GAP3.448.083763735759187899.160.236240.233890.28043RANDOM97.485
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]
4.212.14.21-6.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.009
r_dihedral_angle_3_deg19.627
r_dihedral_angle_4_deg16.589
r_dihedral_angle_1_deg6.007
r_angle_refined_deg1.128
r_scangle_it0.84
r_mcangle_it0.798
r_scbond_it0.485
r_mcbond_it0.439
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.009
r_dihedral_angle_3_deg19.627
r_dihedral_angle_4_deg16.589
r_dihedral_angle_1_deg6.007
r_angle_refined_deg1.128
r_scangle_it0.84
r_mcangle_it0.798
r_scbond_it0.485
r_mcbond_it0.439
r_nbtor_refined0.305
r_nbd_refined0.198
r_symmetry_vdw_refined0.181
r_xyhbond_nbd_refined0.15
r_symmetry_hbond_refined0.083
r_chiral_restr0.077
r_metal_ion_refined0.043
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9422
Nucleic Acid Atoms
Solvent Atoms10
Heterogen Atoms33

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection