5D29 | pdb_00005d29

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a hydroxamate inhibitor JHU241

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	288	34% (v/v) pentaerythritol propoxylate PO/OH 5/4, 2 % (w/v) PEG 3350, and 100 mM Tris-HCl, pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.191	α = 90
b = 130.459	β = 90
c = 157.196	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	100	CCD	RAYONIX MX-225		2013-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.91841	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	1.8	50	99.7	0.062	20.24	5.83		95135	-3	-3

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	1.8	1.91	99.3		0.683	2.72

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1.8	44.82	90374	4757	100	0.1758	0.1743	0.1752	0.2049	0.2049	RANDOM	31.965

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]
1.52			-2.7		1.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.695
r_dihedral_angle_4_deg	15.043
r_dihedral_angle_3_deg	14.602
r_dihedral_angle_1_deg	6.099
r_scangle_it	4.471
r_scbond_it	2.83
r_angle_refined_deg	1.739
r_mcangle_it	1.713
r_mcbond_it	1.016
r_chiral_restr	0.137

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.695
r_dihedral_angle_4_deg	15.043
r_dihedral_angle_3_deg	14.602
r_dihedral_angle_1_deg	6.099
r_scangle_it	4.471
r_scbond_it	2.83
r_angle_refined_deg	1.739
r_mcangle_it	1.713
r_mcbond_it	1.016
r_chiral_restr	0.137
r_bond_refined_d	0.02
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5464
Nucleic Acid Atoms
Solvent Atoms	364
Heterogen Atoms	190

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
XSCALE	data scaling
MAR345dtb	data collection

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.