6RTI

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with aptamer A9g


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62930.2 Mg Acet, 40% (v/v) MPD, 1 mM 2-PMPA
Crystal Properties
Matthews coefficientSolvent content
4.2571.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.096α = 90
b = 121.096β = 90
c = 216.271γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.2105.661000.1640.1720.0480.83810.112.68226636.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.241000.9851.0260.2840.578212.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTFREE R-VALUE2OOT2.2105.6682168403699.9890.1950.1950.1920.217Random44
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]
1.7111.711-3.421
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.279
r_dihedral_angle_3_deg15.204
r_dihedral_angle_4_deg14.367
r_dihedral_angle_1_deg6.937
r_lrange_it6.168
r_lrange_other6.151
r_scangle_it4.632
r_scangle_other4.631
r_mcangle_it3.496
r_mcangle_other3.496
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.279
r_dihedral_angle_3_deg15.204
r_dihedral_angle_4_deg14.367
r_dihedral_angle_1_deg6.937
r_lrange_it6.168
r_lrange_other6.151
r_scangle_it4.632
r_scangle_other4.631
r_mcangle_it3.496
r_mcangle_other3.496
r_scbond_it3.062
r_scbond_other3.062
r_mcbond_it2.344
r_mcbond_other2.344
r_angle_refined_deg1.636
r_angle_other_deg1.374
r_nbd_other0.209
r_symmetry_xyhbond_nbd_refined0.207
r_symmetry_nbd_other0.192
r_nbd_refined0.18
r_nbtor_refined0.176
r_xyhbond_nbd_refined0.162
r_symmetry_nbd_refined0.145
r_symmetry_nbtor_other0.108
r_chiral_restr0.073
r_symmetry_xyhbond_nbd_other0.047
r_bond_refined_d0.007
r_bond_other_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5521
Nucleic Acid Atoms907
Solvent Atoms401
Heterogen Atoms321

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing