2GJS

The crystal structure of human RRAD in complex with GDP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.15M sodium malate, 20% (w/v) PEG 3350, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0740.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.427α = 90
b = 58.56β = 97.18
c = 53.603γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-03-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.95SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.95099.63.924816
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.97100

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 REPLACEMENTTHROUGHOUTswissmodel (first approach mode)1.939.42353623536126699.180.197260.197260.195120.23538RANDOM28.238
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]
0.11-0.611.53-1.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.476
r_dihedral_angle_4_deg17.429
r_dihedral_angle_3_deg15.697
r_dihedral_angle_1_deg6.442
r_scangle_it3.466
r_scbond_it2.28
r_angle_refined_deg1.605
r_mcangle_it1.535
r_mcbond_it1.01
r_angle_other_deg0.948
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.476
r_dihedral_angle_4_deg17.429
r_dihedral_angle_3_deg15.697
r_dihedral_angle_1_deg6.442
r_scangle_it3.466
r_scbond_it2.28
r_angle_refined_deg1.605
r_mcangle_it1.535
r_mcbond_it1.01
r_angle_other_deg0.948
r_symmetry_hbond_refined0.55
r_symmetry_vdw_other0.329
r_metal_ion_refined0.324
r_mcbond_other0.235
r_nbd_refined0.203
r_nbd_other0.195
r_xyhbond_nbd_refined0.185
r_nbtor_refined0.177
r_symmetry_vdw_refined0.166
r_chiral_restr0.086
r_nbtor_other0.084
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
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 Atoms2184
Nucleic Acid Atoms
Solvent Atoms80
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing