4L7Q | pdb_00004l7q

Crystal structure of gamma glutamyl hydrolase (wild-type) from zebrafish

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L9X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	291	30% PEG 4000, 0.1M Sodium citarte tribasic, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 271.61	α = 90
b = 62.05	β = 95.412
c = 123.94	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC QUANTUM 315r		2011-10-01	M	SINGLE WAVELENGTH
2	1	x-ray	110	CCD	ADSC QUANTUM 210r		2011-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13C1	1.0	NSRRC	BL13C1
2	SYNCHROTRON	SPRING-8 BEAMLINE BL12B2	1.0	SPring-8	BL12B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.1	30	97.6			117219	117219

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.1	2.18	97.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	1L9X	2.1	30	111177	111177	5869	95.7	0.23	0.23	0.198	0.2012	0.263	0.2619	RANDOM	30.993

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]
0.01		-0.02	0.09		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.959
r_dihedral_angle_4_deg	20.352
r_dihedral_angle_3_deg	19.126
r_dihedral_angle_1_deg	7.157
r_scangle_it	4.508
r_scbond_it	3.013
c_angle_deg	1.91
r_mcangle_it	1.91
r_mcbond_it	1.086
r_chiral_restr	0.156
c_bond_d	0.023
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13854
Nucleic Acid Atoms
Solvent Atoms	751
Heterogen Atoms	36

Software

Software
Software Name	Purpose
ADSC	data collection
X-PLOR	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
X-PLOR	phasing