1MPL | pdb_00001mpl

CRYSTAL STRUCTURE OF PHOSPHONATE-INHIBITED D-ALA-D-ALA PEPTIDASE REVEALS AN ANALOG OF A TETRAHEDRAL TRANSITION STATE

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3PTE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	298	PEG 8000, SODIUM PHOSPHATE, pH 6.80, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.97	45.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.9	α = 90
b = 66.76	β = 90
c = 100.011	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	100	CCD	ADSC QUANTUM 4	MIRRORS	2001-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12B	0.9999	NSLS	X12B

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	1.12	50	96.6	0.041	27.2	5.5	701505	127013		2

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	1.12	1.16	75.1		0.208	3	2

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R	3PTE	1.12	10	123545	123545	6231	94.2	0.1143	0.1128	0.1143	0.1172	0.14	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
24	225	3081.77

RMS Deviations
Key	Refinement Restraint Deviation
s_non_zero_chiral_vol	0.097
s_approx_iso_adps	0.094
s_zero_chiral_vol	0.087
s_from_restr_planes	0.0334
s_similar_adp_cmpnt	0.031
s_anti_bump_dis_restr	0.03
s_angle_d	0.029
s_bond_d	0.015
s_rigid_bond_adp_cmpnt	0.006
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2601
Nucleic Acid Atoms
Solvent Atoms	445
Heterogen Atoms	51

Software

Software
Software Name	Purpose
SHELXL-97	refinement
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction
CNS	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.