4GYU | pdb_00004gyu

Crystal Structure of New Delhi Metallo-beta-Lactamase-1 A121F mutant from Klebsiella pneumoniae

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3Q6X	PDB entry 3Q6X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	289	0.1 M Imidazole:HCl pH 8.0 1.0 M Sodium Citrate Tribasic, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.473	α = 90
b = 101.473	β = 90
c = 42.679	γ = 120

Symmetry
Space Group	P 65

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 315r	mirrors	2011-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97926	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	50	94.1	0.117	11.4	6.9	22017	22017			14.11

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.83	65.9		0.49	4.2	4.2	769

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3Q6X	1.803	43.939	21999	21999	1131	94.12	0.154	0.154	0.152	0.15	0.195	0.2	random	18.6

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]
3.5887			3.5887		-7.1774

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.386
f_angle_d	1.235
f_chiral_restr	0.096
f_bond_d	0.01
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1796
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms	48

Software

Software
Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	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.