1HVB | pdb_00001hvb

CRYSTAL STRUCTURE OF STREPTOMYCES R61 DD-PEPTIDASE COMPLEXED WITH A NOVEL CEPHALOSPORIN ANALOG OF CELL WALL PEPTIDOGLYCAN

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	298	PEG 8000, sodium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.778	α = 90
b = 66.664	β = 90
c = 100.928	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	BRANDEIS - B4	Monochromator, Mirror	2000-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C	0.9790	NSLS	X12C

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	1.17	20	95.9	0.04	25	5	2330719	111370			18.6

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	1.17	1.21	72.9		0.162	4.6		8392

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	free r	PDB ENTRY 3PTE	1.17	10	111197	111197	5560	96.1	0.1141	0.1141	0.1126	0.1528	RANDOM	16.1

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
35	268.92	3181.8

RMS Deviations
Key	Refinement Restraint Deviation
s_approx_iso_adps	0.102
s_non_zero_chiral_vol	0.091
s_zero_chiral_vol	0.082
s_similar_adp_cmpnt	0.041
s_from_restr_planes	0.0311
s_angle_d	0.03
s_anti_bump_dis_restr	0.026
s_bond_d	0.014
s_rigid_bond_adp_cmpnt	0.006
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2607
Nucleic Acid Atoms
Solvent Atoms	555
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.