5F09

Structure of inactive GCPII mutant in complex with beta-citryl glutamate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4NPG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8288.1533% (v/v) pentaerythritol propoxylate PO/OH 5/4 (Hampton Research, Aliso Viejo, Ca, USA), 1.5% (w/v) PEG 3350 (Merck KGaA, Darmstadt, Germany) and 0.10 M Tris-HCl (Merck KGaA), pH 8.0
Crystal Properties
Matthews coefficientSolvent content
3.3563.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.901α = 90
b = 130.923β = 90
c = 159.136γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2014-07-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.853098.80.0810.08113.294.5189051-335.174
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9697.10.940.9411.964.43

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 REPLACEMENTTHROUGHOUT4NPG1.853084513444499.040.15650.15520.1814RANDOM40.583
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]
0.58-1.691.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.923
r_dihedral_angle_4_deg15.467
r_sphericity_free13.418
r_dihedral_angle_3_deg12.862
r_sphericity_bonded9.865
r_dihedral_angle_1_deg6.176
r_mcangle_it1.695
r_angle_refined_deg1.69
r_mcbond_it1.033
r_mcbond_other1.033
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.923
r_dihedral_angle_4_deg15.467
r_sphericity_free13.418
r_dihedral_angle_3_deg12.862
r_sphericity_bonded9.865
r_dihedral_angle_1_deg6.176
r_mcangle_it1.695
r_angle_refined_deg1.69
r_mcbond_it1.033
r_mcbond_other1.033
r_angle_other_deg1.02
r_chiral_restr0.095
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_gen_planes_other0.004
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5492
Nucleic Acid Atoms
Solvent Atoms562
Heterogen Atoms223

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction
Cootmodel building