2OVJ

The crystal structure of the human Rac GTPase activating protein 1 (RACGAP1) MgcRacGAP.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1F7CPDB entry 1F7C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529825% PEG 3350, 0.1M BIS-TRIS, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1241.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.913α = 90
b = 53.548β = 90
c = 67.979γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.00000SLSX10SA

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
11.4942.0799.90.0750.07573227432274
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)
11.491.5499.30.4915.53134

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1F7C1.4942.073058630586163199.850.153070.153070.151880.17611RANDOM11.767
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]
-0.040.16-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.956
r_dihedral_angle_4_deg16.415
r_dihedral_angle_3_deg11.969
r_dihedral_angle_1_deg11.518
r_scangle_it5.705
r_scbond_it3.928
r_mcangle_it2.912
r_mcbond_it2.183
r_angle_refined_deg1.703
r_angle_other_deg1.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.956
r_dihedral_angle_4_deg16.415
r_dihedral_angle_3_deg11.969
r_dihedral_angle_1_deg11.518
r_scangle_it5.705
r_scbond_it3.928
r_mcangle_it2.912
r_mcbond_it2.183
r_angle_refined_deg1.703
r_angle_other_deg1.05
r_mcbond_other0.578
r_symmetry_vdw_other0.27
r_symmetry_vdw_refined0.255
r_nbd_refined0.242
r_xyhbond_nbd_refined0.202
r_nbd_other0.196
r_nbtor_refined0.185
r_symmetry_hbond_refined0.156
r_chiral_restr0.112
r_nbtor_other0.088
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1562
Nucleic Acid Atoms
Solvent Atoms171
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing