2QE0 | pdb_00002qe0

Thioacylenzyme Intermediate of GAPN from S. Mutans, New Data Integration and Refinement.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ESD	PDB ENTRY 2ESD

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 142.47	α = 90
b = 155.21	β = 90
c = 113.08	γ = 90

Symmetry
Space Group	P 21 21 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	MAR CCD 165 mm		2002-06-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.98040	ESRF	BM30A

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	2.19	19.78	99.7	0.087	17.4	7.1		124421		3	36.03

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	2.19	2.33	99.5		0.393	3.9	4.8	17938

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 2ESD	2.19	19.78	124377	12452	96.52	0.1889	0.1843	0.19	0.2299	0.23	RANDOM	32.32

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]
4.85464586			-7.58909516		2.7344493

RMS Deviations
Key	Refinement Restraint Deviation
t_dihedral_angle_d	19.807
t_it	1.291
t_angle_deg	1.285
t_nbd	0.071
t_gen_planes	0.018
t_bond_d	0.011
t_trig_c_planes	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14368
Nucleic Acid Atoms
Solvent Atoms	1384
Heterogen Atoms	232

Software

Software
Software Name	Purpose
BUSTER-TNT	refinement
MAR345dtb	data collection
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.