6RTI

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OOT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	0.2 Mg Acet, 40% (v/v) MPD, 1 mM 2-PMPA

Crystal Properties
Matthews coefficient	Solvent content
4.25	71.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.096	α = 90
b = 121.096	β = 90
c = 216.271	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2017-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.2	105.66	100	0.164	0.172	0.048	0.838	10.1	12.6		82266			36.3

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)	Redundancy	Number Unique Reflections (All)
1	2.2	2.24	100		0.985	1.026	0.284	0.578	2	12.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2OOT	2.2	105.66	82168	4036	99.989	0.195	0.195	0.192	0.217	Random	44

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]
1.711			1.711		-3.421

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.279
r_dihedral_angle_3_deg	15.204
r_dihedral_angle_4_deg	14.367
r_dihedral_angle_1_deg	6.937
r_lrange_it	6.168
r_lrange_other	6.151
r_scangle_it	4.632
r_scangle_other	4.631
r_mcangle_it	3.496
r_mcangle_other	3.496
r_scbond_it	3.062
r_scbond_other	3.062
r_mcbond_it	2.344
r_mcbond_other	2.344
r_angle_refined_deg	1.636
r_angle_other_deg	1.374
r_nbd_other	0.209
r_symmetry_xyhbond_nbd_refined	0.207
r_symmetry_nbd_other	0.192
r_nbd_refined	0.18
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.162
r_symmetry_nbd_refined	0.145
r_symmetry_nbtor_other	0.108
r_chiral_restr	0.073
r_symmetry_xyhbond_nbd_other	0.047
r_bond_refined_d	0.007
r_bond_other_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5521
Nucleic Acid Atoms	907
Solvent Atoms	401
Heterogen Atoms	321

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing