3NCK | pdb_00003nck

Crystal Structure of BlaC-E166A covalently bound with Nafcillin

X-RAY DIFFRACTION

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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	VAPOR DIFFUSION, SITTING DROP	7.5	298	0.1 M HEPES, 2 M NH4H2PO4, pH 7.5, Vapor diffusion, Sitting drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.671	α = 90
b = 67.822	β = 90
c = 76.643	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		2009-09-26		SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 210		2009-09-26		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C	1.000	NSLS	X12C
2	SYNCHROTRON	NSLS BEAMLINE X29A	1.000	NSLS	X29A

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	2.8	50.79	99.8	0.152	12.1	5.9		6626

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	2.8	2.874	93.89		0.606	1.9	5.9	327

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	2.8	50	6599	309	99.4	0.188	0.185	0.1852	0.265	0.2625	RANDOM	34.813

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]
1.16			-1.26		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.051
r_dihedral_angle_4_deg	25.597
r_dihedral_angle_3_deg	15.522
r_dihedral_angle_1_deg	6.2
r_scangle_it	2.76
r_scbond_it	1.554
r_angle_refined_deg	1.391
r_mcangle_it	1.244
r_mcbond_it	0.658
r_chiral_restr	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1914
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling