4NGM

Crystal Structure of Glutamate Carboxypeptidase II in a complex with urea-based inhibitor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop	8	289	Tris-HCl, PEG 3350, pentaerythritol propoxylate, pH 8.0, hanging drop, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.15	60.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.3	α = 90
b = 130.193	β = 90
c = 158.789	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	MARMOSAIC 225 mm CCD	mirrors			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	1.84	49.032	99	0.068	11.31			90745		2	28.155

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)	Redundancy	Number Unique Reflections (All)
1	1.84	1.95	98.9		0.467	0.591	1.91

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.84	49.03	90744	4538	99.72	0.1714	0.1696	0.2057	RANDOM	27.4037

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			-2.15		1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.488
r_dihedral_angle_4_deg	15.732
r_dihedral_angle_3_deg	13.957
r_dihedral_angle_1_deg	6.108
r_mcangle_it	3.014
r_mcbond_it	2.298
r_mcbond_other	2.292
r_angle_refined_deg	1.969
r_angle_other_deg	0.933
r_chiral_restr	0.119

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.488
r_dihedral_angle_4_deg	15.732
r_dihedral_angle_3_deg	13.957
r_dihedral_angle_1_deg	6.108
r_mcangle_it	3.014
r_mcbond_it	2.298
r_mcbond_other	2.292
r_angle_refined_deg	1.969
r_angle_other_deg	0.933
r_chiral_restr	0.119
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5517
Nucleic Acid Atoms
Solvent Atoms	598
Heterogen Atoms	252

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.