6HKZ

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a inhibitor RNA 2-49-1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BI1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	33% (v/v) pentaerythritol propoxylate PO/OH 5/4 2 % (w/v) PEG 3350 100 mM Tris-HCl, pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
3.45	64.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.956	α = 90
b = 132.259	β = 90
c = 161.589	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	PIXEL	DECTRIS PILATUS 6M		2017-08-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.918	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.09	50	99.2	0.091	12.56	4.5		64380

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.09	2.21	97.4		0.666	2.05	4.6

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	3BI1	2.09	47.59	63218	2100	99.25	0.17148	0.17043	0.20308	RANDOM	57.595

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]
1.86			-3.67		1.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.391
r_dihedral_angle_4_deg	16.85
r_dihedral_angle_3_deg	15.205
r_dihedral_angle_1_deg	6.571
r_long_range_B_refined	6.168
r_long_range_B_other	6.168
r_scangle_other	5.155
r_mcangle_it	3.626
r_mcangle_other	3.626
r_scbond_it	3.574
r_scbond_other	3.573
r_mcbond_it	2.762
r_mcbond_other	2.761
r_angle_refined_deg	1.656
r_angle_other_deg	0.67
r_chiral_restr	0.074
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	5529
Nucleic Acid Atoms
Solvent Atoms	319
Heterogen Atoms	211

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
REFMAC	phasing