4W79 | pdb_00004w79

Crystal Structure of Human Protein N-terminal Glutamine Amidohydrolase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	291	PROTEIN SOLUTION (10 MG/ML SE-MET PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, BIS-TRIS PH 7.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (1% ETHYLENE GLYCOL, 1.8 M AMMONIUM SULFATE, 0.10 M MES PH 6.0). CRYOPROTECTED IN FOUR STAGES WITH WELL SOLUTION USING 0 TO 25 % ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.322	α = 90
b = 64.039	β = 90
c = 113.66	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	MARMOSAIC 300 mm CCD		2008-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97942	APS	23-ID-D

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	100	99.5	0.105	8.9	12.2		40943

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	1.53	95.9		0.543		6.9	2566

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		THROUGHOUT	1.5	56.83	38673	2045	98.82	0.145	0.1437	0.1436	0.1699	0.1694	RANDOM	17.19

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]
0.27			0.21		-0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.089
r_dihedral_angle_4_deg	15.171
r_dihedral_angle_3_deg	13.293
r_dihedral_angle_1_deg	8.007
r_mcangle_it	3.667
r_mcbond_it	2.594
r_mcbond_other	2.559
r_angle_refined_deg	1.913
r_angle_other_deg	0.847
r_chiral_restr	0.113
r_bond_refined_d	0.017
r_gen_planes_refined	0.016
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1632
Nucleic Acid Atoms
Solvent Atoms	332
Heterogen Atoms	75

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction