2QMC | pdb_00002qmc

Crystal Structure of Helicobacter Pylori Gamma-Glutamyltranspeptidase T380A Mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NQO	pdb entry 2NQO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	200 MM HEPES, 25% PEG MME2000, 5 MG/ML PROTEIN, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.14	α = 90
b = 106.674	β = 104.96
c = 87.194	γ = 90

Symmetry
Space Group	P 1 21 1

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	ADSC QUANTUM 315		2007-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9	APS	14-BM-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.55	50	93.2	0.084	0.068	21.3	6.6		135161

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.61	89		0.538	0.413	2.59	5	12852

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 2NQO	1.55	33.35	134438	13319	92.65	0.19	0.187	0.1858	0.218	0.2161	RANDOM	21.126

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]
1.29		0.03	-1.25		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.836
r_dihedral_angle_4_deg	14.798
r_dihedral_angle_3_deg	12.449
r_dihedral_angle_1_deg	6.132
r_scangle_it	2.864
r_scbond_it	1.86
r_angle_refined_deg	1.354
r_mcangle_it	0.993
r_mcbond_it	0.685
r_nbtor_refined	0.304
r_nbd_refined	0.196
r_symmetry_vdw_refined	0.188
r_symmetry_hbond_refined	0.119
r_xyhbond_nbd_refined	0.101
r_chiral_restr	0.086
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8029
Nucleic Acid Atoms
Solvent Atoms	588
Heterogen Atoms	30

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
MOLREP	phasing