3M6B | pdb_00003m6b

Crystal Structure of the Ertapenem Pre-isomerized Covalent Adduct with TB B-lactamase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DWZ	pdb entry 3DWZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop	4.1	298	0.1 M HEPES, 2 M NH4(H2)PO4, pH 4.1, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.657	α = 90
b = 67.922	β = 90
c = 75.546	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 210		2010-01-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C	1.100	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	1.3	50	100	0.057	21.4	7.5	63485	63485

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	1.3	1.33	100		0.757	1.8	5.7	4388

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 3DWZ	1.3	26.28	60263	3222	99.96	0.149	0.147	0.15	0.176	0.17	RANDOM	13.287

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]
0.03			-0.04		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.298
r_dihedral_angle_4_deg	21.341
r_dihedral_angle_3_deg	11.508
r_dihedral_angle_1_deg	6.091
r_scangle_it	4.451
r_scbond_it	3.009
r_mcangle_it	1.959
r_angle_refined_deg	1.428
r_rigid_bond_restr	1.292
r_mcbond_it	1.198

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.298
r_dihedral_angle_4_deg	21.341
r_dihedral_angle_3_deg	11.508
r_dihedral_angle_1_deg	6.091
r_scangle_it	4.451
r_scbond_it	3.009
r_mcangle_it	1.959
r_angle_refined_deg	1.428
r_rigid_bond_restr	1.292
r_mcbond_it	1.198
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1988
Nucleic Acid Atoms
Solvent Atoms	297
Heterogen Atoms	61

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
DENZO	data reduction
SCALEPACK	data scaling

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.