3BI1

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a transition state analog of methotrexate-Glu

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	8	293	33% (v/v) pentaerythritol propoxylate PO/OH 5/4, 1% (w/v) PEG 3350, 100 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.33	63.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.116	α = 90
b = 130.462	β = 90
c = 159.456	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 300 mm CCD		2006-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00	APS	22-ID

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	1.5	30	99.5	0.085	19	10	169309	169309	-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	1.5	1.55	98.2		0.62	2.2	6.6

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	2oot	1.5	15	166133	1683	99.31	0.14858	0.14838	0.16892	RANDOM	27.094

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]
0.8			-1.65		0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.922
r_dihedral_angle_4_deg	14.395
r_dihedral_angle_3_deg	14.277
r_sphericity_free	9.398
r_sphericity_bonded	7.639
r_dihedral_angle_1_deg	5.64
r_scangle_it	5.207
r_scbond_it	3.727
r_mcangle_it	2.774
r_rigid_bond_restr	2.258
r_mcbond_it	1.961
r_angle_refined_deg	1.768
r_nbtor_refined	0.325
r_symmetry_hbond_refined	0.271
r_symmetry_vdw_refined	0.243
r_nbd_refined	0.226
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.129
r_metal_ion_refined	0.065
r_bond_refined_d	0.02
r_gen_planes_refined	0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5529
Nucleic Acid Atoms
Solvent Atoms	710
Heterogen Atoms	209

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling