5CFY

CRYSTAL STRUCTURE OF GLTPH R397A IN COMPLEX WITH NA+ AND L-ASP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NWX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5277PEG400, SODIUM CHLORIDE, CITRATE/TRIS
Crystal Properties
Matthews coefficientSolvent content
4.673.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.958α = 90
b = 116.958β = 90
c = 313.517γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.97NSLSX29A

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
13.51598.10.08410.64.555613
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.53.6396.60.44.2

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 REPLACEMENTTHROUGHOUT2NWX3.51555613295597.10.2510.2490.294RANDOM152.9
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]
-4.35-2.18-4.3514.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.106
r_dihedral_angle_3_deg23.919
r_dihedral_angle_4_deg10.548
r_long_range_B_refined8.692
r_long_range_B_other8.691
r_dihedral_angle_1_deg7.784
r_mcangle_it5.591
r_mcangle_other5.591
r_scangle_other5.149
r_mcbond_it3.457
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.106
r_dihedral_angle_3_deg23.919
r_dihedral_angle_4_deg10.548
r_long_range_B_refined8.692
r_long_range_B_other8.691
r_dihedral_angle_1_deg7.784
r_mcangle_it5.591
r_mcangle_other5.591
r_scangle_other5.149
r_mcbond_it3.457
r_mcbond_other3.457
r_scbond_it2.953
r_scbond_other2.953
r_angle_other_deg2.266
r_angle_refined_deg2.017
r_chiral_restr0.115
r_bond_refined_d0.019
r_bond_other_d0.015
r_gen_planes_refined0.008
r_gen_planes_other0.008
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms18168
Nucleic Acid Atoms
Solvent Atoms6
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building