5CIW

Ran GDP Y39A mutant monoclinic crystal form


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.229134 % PEG 1000, 50 mM HEPES pH 7.2, 20 mM MgCl2, 1 mM BeF
Crystal Properties
Matthews coefficientSolvent content
2.4541.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.9α = 90
b = 59.33β = 96.55
c = 64.79γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2009-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9840SLSX10SA

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
11.7519.89194.70.03423.423.6441838
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)
11.751.880.30.2753.02

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 REPLACEMENTTHROUGHOUThuman Ran GDP1.7519.8939744209294.750.201150.198790.24636RANDOM30.747
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]
0.090.05-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.889
r_dihedral_angle_3_deg17.736
r_dihedral_angle_4_deg13.627
r_long_range_B_refined7.13
r_dihedral_angle_1_deg6.768
r_scbond_it4.137
r_mcangle_it4.057
r_mcbond_it3.049
r_angle_refined_deg2.164
r_chiral_restr0.175
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.889
r_dihedral_angle_3_deg17.736
r_dihedral_angle_4_deg13.627
r_long_range_B_refined7.13
r_dihedral_angle_1_deg6.768
r_scbond_it4.137
r_mcangle_it4.057
r_mcbond_it3.049
r_angle_refined_deg2.164
r_chiral_restr0.175
r_bond_refined_d0.02
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
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 Atoms3182
Nucleic Acid Atoms
Solvent Atoms113
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing